An Introduction to Decalcification

23. October 2012

Decalcification describes the technique for removing mineral from bone or other calcified tissue so that good-quality paraffin sections can be prepared that will preserve all the essential microscopic elements. Decalcification is carried out after the specimen has been thoroughly fixed and prior to routine processing to paraffin. In this paper the basic structure of bone is described and the technical options for preparing sections are outlined. The procedure for decalcification and the successful monitoring of the process is discussed and some popular options for the choice of reagents are provided.

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There are a number of options available when the histologist is required to produce sections from bone or other calcified specimens. In choosing a technique and processing method consideration must be given to the type of investigation being carried out. For example if a metabolic bone disease is being investigated and it is necessary to differentiate mineralized bone from osteoid, or if morphometric measurements are required, it may be necessary to retain and demonstrate the mineral content by producing sections of “un-decalcified” bone. As mineralized bone is such a hard material there are a limited range of techniques available to produce sections from it. After fixation it can be directly sawn into thin wafers and then ground using abrasive surfaces to produce thin “ground” sections (see Figure 1). It is also possible to prepare bone specimens by infiltrating them with acrylic or epoxy resins which, when polymerized, have a hardness equivalent to that of mineralized bone. You can then produce ground sections from the infiltrated specimens or section them directly using a heavy-duty microtome (such as the Leica SM2500) and a tungsten-carbide or diamond knife (see Figure 2). Frozen sections of mineralized cancellous bone are another possibility.1-3

Figure 1: An unstained ground section of compact bone. A number of osteons (Haversian systems) are cut transversely. The osteons consist of concentric layers of bone (lamelle) surrounding a central Haversian canal containing blood vessels. Within the lamelle are lacunae (spaces) normally containing osteocytes. In dried ground sections such as this they appear as black structures due to particles of abrasive and air contained within them.
Figure 2: An un-decalcified section of cancellous bone (Von Kossa). The bone was fixed in formalin and processed and embedded in epoxy resin for sectioning. Calcified bone is black and a rim of osteoid on the surface of the trabeculae is stained blue as are the components of the bone marrow. Note that despite the support of polymerized resin, in this case the calcified matrix has cracked during preparation of the section.

Much more commonly bone and other calcified specimens are decalcified (demineralised) following fixation and processed using a standard method to produce paraffin sections. Decalcified sections are used for the examination of bone marrow and for the diagnosis of tumours, infections or for other purposes. The specimens may be in the form of iliac crest trephines or bone pieces removed at operation (such as femoral heads) or dissected from amputation specimens. Fine detail radiographs are often used to assist in the selection of appropriate bone specimens for processing. Apart from bone, other tissues may undergo calcification associated with degenerative processes such as necrosis (dystrophic calcification) or it may occur in the walls of blood vessels or in kidney, lung or elsewhere (metastatic calcification).4 If the calcified areas in tissue specimens are substantial it may be impossible to obtain decent sections without first decalcifying the specimen. Another possibility, is to apply “surface decalcification” to a paraffin block to allow sections to be obtained where the presence of calcium was not anticipated when the specimen was processed.

The decalcification procedure is relatively straightforward and is extensively discussed in standard texts of histological technique. 1-3 If high quality results are to be obtained however, some points are worthy of emphasis.

Structure of bone

Bone consists of cells (osteocytes) surrounded by a calcified matrix containing Type 1 collagen fibres. In the matrix calcium is in the form of hydroxyapatite crystals [Ca10(PO4)6(OH)2] which are deposited between the fibrous elements. These crystals are dissolved out during the process of decalcification which, if performed correctly, leaves cohesive tissue with the physical characteristics of dense fibrous connective tissue.

There are two types of mature bone. Cortical or compact bone forms the shafts of long bones and the major parts of the flat bones of the skull and has a very dense structure based on an arrangement of cylindrical structures called osteons (Figure 3). Cancellous, trabecular or spongy bone has a much more delicate arrangement consisting of thin partitions (trabeculae) connecting bony plates between which is found the bone marrow. It is located in the vertebra and at the epiphyses of long bones (Figure 4). Both compact and cancellous bone develop in layers or lamelle in which the collagen fibres are structurally orientated and show a characteristic picture under polarized-light microscopy (see Figure 5).2-3, 5

Figure 3: A transverse section from a long bone optimally decalcified using formic acid (H&E). Numerous osteons with peripheral cement lines are shown. Well-stained osteocyte nuclei are present indicating that the decalcification endpoint was not exceeded.
Figure 4: A decalcified section of cancellous bone (pink) and hyaline cartilage (blue) from the epiphysis of a long bone (H&E). The delicate trabeculae of the bone are well preserved as is the fine structure of the bone marrow and associated adipocytes. The basophilic/acidophilic balance of the stain is well maintained indicating that the formic acid decalcification was optimal.
Figure 5: A decalcified section of compact bone from the shaft of a long bone (H&E). The section is photographed under polarized light to demonstrate the concentric lamelle forming the osteons. The birefringence is due to the orientation of collagen fibres in the bone matrix which differs between successive layers.

It is important to carefully consider the nature of any bone specimen received for processing because the relative amounts of cortical and cancellous bone are important and will determine the time required for decalcification and processing. For example, the iliac crest trephine specimen consists of a rim of cortical bone overlying a cylinder of cancellous bone. The cortical bone will be the last to give up its calcium salts during decalcification and unless it is completely decalcified difficulty will be experienced in obtaining decent sections.

Fixation of bone

In order to protect the cellular and fibrous elements of bone from damage caused by the acids used as decalcifying agents, it is particularly important to thoroughly fix these specimens prior to decalcification. 2-3 Poorly-fixed specimens become macerated during decalcification and stain poorly afterwards. This is very noticeable in areas containing bone marrow. It is therefore common practice for laboratories to extend fixation times for bone specimens before commencing decalcification. It is important to provide ready access for the fixative to penetrate the bone, so skin and soft tissue should be removed from large specimens if practicable. Bone specimens should be sawn into thin slices as soon as possible to enhance fixation and an adequate volume of fixative provided. High-quality fine tooth saws should be used to prepare bone slices. Coarse saws can cause considerable mechanical damage and force bone fragments into the soft tissues present in the specimen (see Figure 6).

Buffered formalin is a satisfactory fixative for bone but where the preservation of bone marrow is important some laboratories will use alternatives such as one of the Zinc formalin mixtures, B5, formol acetic alcohol (Davidson’s fixative), or Bouin.

Figure 6: A trephine specimen in which bone fragments have been forced into the marrow spaces during preparation (arrows). This is an un-decalcified resin section stained with Von Kossa’s method to demonstrate calcium.

Decalcifying agents – Overview

There are three main types of decalcifying agents:

For convenience most laboratories choose from the many proprietary reagents available. Potential users of these products should consult the relevant MSDS to determine the active component present if it is not clearly stated in the technical information provided.

Decalcifying agents – Strong acids

Strong acids such as hydrochloric or nitric acid at concentrations up to 10% are the most rapid in action but if used for an excessive time will rapidly cause a loss of nuclear staining and can macerate tissues. It is important that an appropriate end-point test is used to minimise exposure of the specimens to these agents. Generally proprietary decalcifiers that are claimed to be rapid in action are based on strong acids, most commonly hydrochloric acid, and should be used conservatively with attention to the provided instructions if good results are to be obtained. For example Surgipath’s Decalcifier II®  is rapid in action and contains hydrochloric acid. Figure 7 demonstrates the consequences of prolonged treatment with a mineral acid decalcifier beyond the appropriate end-point.

Table 1 lists several of the more common mineral acid-based decalcifiers. Standard textbooks of histotechnology should be consulted for a more comprehensive listing.

Table 1: Mineral acid decalcifiers




Nitric acid6

5% in distilled water

Rapid in action, exceeding end-point will impair staining.

Perenyi’s fluid6 (1882)

10% nitric acid 40ml

0.5% chromic acid 30ml

Absolute alcohol 30ml

A traditional decalcifier that decalcifies more slowly than aqueous nitric acid. Quite rapid in action, exceeding end-point will impair staining.

Hydrochloric acid3

5-10% in distilled water

Formalin should be washed from specimen before placing in HCl to avoid the formation of bis-chloromethyl ether (a carcinogen). Rapid in action, exceeding end-point will impair staining.

Von Ebner’s solution6

Sodium chloride saturated soln. 50ml

Distilled water 42ml

Hydrochloric acid 8ml

Rapid in action, exceeding end-point will impair staining.

Figure 7: A section of decalcified cancellous bone (H&E). This specimen was decalcified with a hydrochloric acid decalcifier for an excessive time without using an appropriate endpoint test. Although the tissue elements are cohesive the staining is very poor showing a complete absence of nuclear staining together with strong, poorly-differentiated eosin.

Decalcifying agents – Weak acids

Weak acids such as formic acid are popular and are widely used for decalcification. Formic acid can be used as a simple 10% aqueous solution or combined with formalin or with a buffer. Although it is slower than the strong acid agents it is much gentler in action and less likely to interfere with nuclear staining. 1, 7 An example of a proprietary decalcifier based on formic acid is Surgipath’s Decalcifier I®. It also contains formalin and is claimed to fix as well as decalcify and be gentle in action. Other acids such as trichloracetic acid (TCA) have also been used. Picric acid, as a component of some fixatives has weak decalcifying properties.

Table 2: Weak acid decalcifiers




Formic acid8

10% in distilled water

A simple effective decalcifier.

Evans and Krajian8

Formic acid 25ml

Sodium citrate 10g

Distilled water 75ml

An effective formic acid decalcifier buffered with citrate.


Formic acid 18ml

Sodium formate 3.5g

Distilled water 82ml

An effective formic acid decalcifier buffered with formate

Gooding and Stewart8

Formic acid 5-25ml

40%formaldehyde 5ml

Distilled water 75ml

A formic acid decalcifier with added formalin, claimed to fix and decalcify.

Decalcifying agents – Chelating agents

Chelating agents such as ethylenediaminetetracetic acid (EDTA), work by capturing the calcium ions from the surface of the apatite crystal, slowly reducing its size. Because the process is very slow but very gentle (weeks may be required depending on the size of the specimen), this reagent is not suitable for urgent specimens but more appropriate for research applications where very high quality morphology is required or particular molecular elements must be preserved for techniques such as IHC, FISH or PCR.9 It is used at a concentration of approximately 14% as a neutralized solution.1,10 The rate at which EDTA will decalcify is pH dependent. It is generally used at pH7.0. It works more rapidly at pH10 but some tissue elements can be damaged at alkaline pH. 10


Table 3: Chelating agents




Neutral EDTA1

EDTA disodium salt 250g

Distilled water 1750ml

Bring to pH 7.0 by adding sodium hydroxide (about 25g will be needed).

Acts slowly but causes little tissue damage. Conventional stains are largely unaffected.

Factors influencing the rate of decalcification

The concentration of active agent will affect the rate at which calcium is removed. Published formulations for decalcifying solutions strike a balance between speed and degree of tissue damage. It must be remembered that the concentration of active agent will be depleted as it combines with calcium and so it is wise to use a large volume of decalcifier and renew it several times during the decalcification process.

Increased temperature will speed up the decalcification rate but will also increase the rate of tissue damage so must be employed with great care.

Gentle agitation may increase the rate slightly.1

Fluid access.
As with fixation fresh decalcifier should have ready access to all surfaces of the specimen. This will enhance diffusion and penetration into the specimen and facilitate solution, ionization and removal of calcium.

Other techniques for increasing the efficiency of decalcification

Sonication used with EDTA has been successfully used to accelerate decalcification of trephine specimens for subsequent molecular analysis. During the process the temperature must be carefully controlled.9 Microwave treatment has been used with hydrochloric acid decalcifiers but the raised temperature may damage morphology and cause staining artefacts.10 Ion-exchange resins have been incorporated into some decalcification protocols. They are added to the container holding the decalcifier and take up the ionized calcium maintaining the effectiveness of the acid. If acid decalcifiers are used in adequate volumes and replaced regularly the use of such resins is probably unnecessary.3 Electrolytic decalcification in which the bone is placed in acid decalcifier and attached to an electrode through which current is applied is a technique that has not found wide acceptance because of the potential to cause heat damage to the specimen.3

Determining the end-point of decalcification

If high-quality results are to be obtained it is important to determine the point at which all the calcium has been removed, because, from this point on, tissue damage seems to occur at an increasing rate. Over-decalcification, particularly with the strong acid decalcifiers, spoils the staining of basophilic elements such as cell nuclei and in some circumstances can cause maceration of the softer tissue elements. On the other hand specimens that are incompletely decalcified may be difficult or impossible to section.

The best method, particularly with large specimens such as femoral heads, is to X-ray the specimen. A good-quality X-ray will clearly reveal tiny residual calcium deposits and allow further treatment if required. It is an excellent method for following the process of decalcification of large specimens such as femoral heads (see Figure 8). A simple chemical test can be applied when some acid decalcifiers are used (particularly formic acid). Ammonium oxalate solution is added to a sample of the final change of decalcified that has been neutralized with ammonium hydroxide.1 If calcium is present a precipitate of calcium oxalate will form indicating that decalcification is probably incomplete and a longer time in decalcified is required. Of course this test is best done on a relatively recent change of decalcifier (exposed to the tissue for say, one hour only). Physical tests require manipulation, bending probing or trimming of the specimen to “feel” for remaining calcified areas. Whilst this method may be successful in experienced hands it is generally considered to be unreliable. Mechanical damage can occur during bending or probing and small deposits of calcium can easily be missed.7 A method of determining the endpoint by carefully weighing the specimen after rinsing and blotting has also been described. This may be an effective method for large specimens.10

If you believe the decalcification end-point is close and you wish to slow the process down so as to avoid over-decalcification and consequent tissue damage, as might be the case when your laboratory is unoccupied during a weekend, specimens can be removed from decalcifier, rinsed and placed back into formalin (important if hydrochloric acid is being used). Decalcification can then be resumed when convenient.10 An alternative is to refrigerate the specimen at 4˚C in its decalcifier to slow down the process.1

Figure 8: An X-ray series following the process of decalcification of a femoral head with formic acid/citrate decalcifier. The radiographs were produced using a Hewlett-Packard Faxitron® and allow the process to be accurately followed and the endpoint to be properly identified.
Figure 9: A decalcified paraffin section of fibula (H&E). Note the size of the specimen. It was decalcified with a formic acid agent using a chemical endpoint test then processed to paraffin using an extended schedule. The 13 y/o male sustained a pathologic fracture of his right fibula after a fall. X-ray showed bony enlargement of the mid-shaft of the (R) fibula. Pathologic diagnosis was bone cyst with pathologic fracture. The section was prepared in the bone laboratory of the Armed Forces Institute of Pathology (USA) in 1983.

Treatment following decalcification and prior to processing

Various methods for neutralizing residual acid decalcifier before processing have been published, including extensive washing in tap water or the application of alkaline solutions. Generally a short, effective wash in tap water should be sufficient as any remaining acid will be removed during processing.1 It is important to remove the bulk of the decalcifier to avoid contaminating the processing reagents and the processor with acid.

Choosing a suitable schedule for decalcified bone or other decalcified tissues

Once the mineral has been removed a standard processing schedule can be used. It must be borne in mind that despite complete decalcification, bone, particularly compact bone, will contain dense areas that require thorough processing. It is better to use a schedule which is too long than too short. Your choice will depend on the nature and size of the specimen. Application of vacuum during wax infiltration should improve the quality of the finished blocks.

Surface decalcification

This is a method of dealing with small unexpected deposits of calcium that may be encountered in paraffin blocks (see Figure 10). Normally it is after trimming the block in the microtome to expose the specimen that the calcium is discovered. It is important at this stage to try to avoid disrupting the block surface extensively. After the tissue has been exposed the block can be removed from the microtome and placed face down in an acid decalcifier for 15 – 60 minutes. This surface treatment will allow the decalcifier to penetrate a small distance into the block and dissolve the calcium. The block can then be thoroughly rinsed in water to remove residual acid, chilled and sectioned. Careful realignment of the block will be required because the decalcifier will penetrate a very small distance into the block allowing only a couple of sections to be taken.1, 11

Figure 10: A section from a granuloma specimen in which unanticipated calcium deposits were encountered (blue). Sections of better quality could have been prepared if surface decalcification had been applied to this block.


Decalcification is a straightforward process but to be successful requires:

  • A careful preliminary assessment of the specimen
  • Thorough fixation
  • Preparation of slices of reasonable thickness for fixation and processing
  • The choice of a suitable decalcifier with adequate volume, changed regularly
  • A careful determination of the endpoint
  • Thorough processing using a suitable schedule.


  1. Page KM. Bone. In Bancroft JD and Stevens A eds. Theory and Practice of Histological Techniques. New York: Churchill Livingstone, 1996.
  2. Moore RJ. Bone. In Woods AE and Ellis RC eds. Laboratory histopathology. New York: Churchill Livingstone, 1994;7.2-10.
  3. Carson FL. Histotechnology. 2nd ed. Chicago: ASCP Press, 2007.
  4. Vardaxis NJ. Pathology for the health sciences. Melbourne: Macmillan Australia Pty Ltd, 1997.
  5. Young B, Heath JW. Wheater's Functional Histology. 4th ed. Edinburgh: Churchill Livingstone, 2000.
  6. Clayden EC. Practical section cutting and staining. Edinburgh: Churchill Livingstone, 1971.
  7. Skinner RA, Hickmon SG, Lumpkin CK, Aronson J, Nicholas RW. Decalcified Bone: Twenty Years of Successful Specimen Management. The Journal of Histotechnology 1997;20;267-277.
  8. Wallington EA. Histological Methods for Bone. London: Butterworths, 1972.
  9. Reineke T, Jenni B, Abdou MT et al. Ultrasonic Decalcification Offers New Perspectives for Rapid FISH, DNA, and RT_PCR Ananlysis in Bone Marrow Trephines Am J Surgical Pathology 2006;30.
  10. Callis G, Sterchi D. Decalcification of Bone: Literature Review and Practical Study of Various Decalcifying Agents, Methods, and Their Effects on Bone Histology. The Journal of Histotechnology 1998;21;49-58.
  11. Rolls GO. Difficult Blocks and Reprocessing. Leica Microsystems, 2011.


Geoffrey Rolls

Geoffrey Rolls, Histology Consultant, Leica Biosystems, Melbourne, Australia, has extensive experience practicing and teaching histology and histotechnology including 30 years as Senior Lecturer in the Department of Laboratory Medicine at RMIT University in Melbourne, Australia. He holds a science degree and a professional Fellowship of the Australian Institute of Medical Scientists. He has a broad interest in histotechnology, particularly in the areas of tissue processing and microtomy and in general histology education. For the last ten years he has acted as a consultant to Leica Biosystems.

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