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VHA Diagnostic Electron Microscopy Program

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Before discussing Current Procedural Terminology (CPT) coding for Electron Microscopy, it is useful to review the major different types of studies done in a hospital Electron Microscopy Laboratory for diagnosis. The majority of studies are done using a Conventional Transmission Electron Microscope (CTEM) and involve studying the ultrastructure of thin sections of tissue such as kidney biopsies and certain tumors. In order to select an appropriate area for thin section study, so called "thick" sections of plastic embedded tissue must first be examined by light microscopy. These "thick" sections are actually only ¼ to ½ micron thick, but they are much thicker than the thin sections used in the electron microscope. Sometimes negatively stained samples such as viral suspensions are examined in a CTEM. While the specimen preparation for these samples is completely different from the usual plastic embedding technique, the microscopy operations on the electron microscope are quite similar, and the amount of professional time and professional expertise needed to interpret these is just as great.

In recent years an increasing number of samples have been examined in a scanning electron microscope (SEM). Most of these samples are examined in an SEM equipped with an energy dispersive x-ray spectrometer (EDX), which permits the observer to obtain morphologic information and chemical data on the sample. The major application area is in the diagnosis of asbestosis and other pneumoconioses. On rare occasions the SEM can be used without the x-ray detector for diagnostic morphologic studies such as for genetic abnormalities concerning the shape of individual hairs.

Prior to 2015 the CPT coding book available from the AMA referred to two different types of CPT codes for charges in electron microscopy. The first of these is "electron microscopy, diagnostic" (88348). The second of these was indented below the first, and had the name of "scanning" (88349). In 2015 the latter code (88349) was deleted. Currently this first and now only code "88348" should be used for all studies that include CTEM as well as for specimens studied by secondary electron imaging, scanning transmission electron microscopy, or microprobe analysis.

The above comments are based solely on the AMA coding book. If, however, one considers reimbursement by Medicare, then another complication may arise. In the past, in some states, Medicare has not recognized (has not paid for) 88349. In those areas one should probably use 88348 for SEM/EDX specimens.  Another issue concerns "thick sections".  Medicare does recognize, and does pay for 88313, which codes for "all other" special stains, such as iron and trichrome (but not immunohistochemistry). Since toluidine blue fits the definition of a special stain, some laboratories bill 88313 for cases examined by thick sections alone. Furthermore, if a CTEM report mentions the review of the toluidine blue stained sections in the body of the CTEM report, then some laboratories bill both 88348 and 88313 for all routine CTEM cases. If review of the toluidine blue sections is done, but not documented in the report, then only 88348 can be billed.

This is a complex subject, and there are regional differences. It is not clear why in some areas it is acceptable to bill both 88348 and 88313, whereas in other areas it is not acceptable to bill both, but these appear to be current practices.

Below are given some examples of typical specimens studied in our laboratory, with examples of possible CPT coding for the case indicated:

1. A kidney biopsy studied by light microscopy (paraffin sections), electron microscopy and direct immunofluorescence - 88305, 88348 and 88346.

2. A heart biopsy studied by light microscopy and electron microscopy - 88307 and 88348, or 88307, 88313 and 88348.

3. A nerve biopsy studied by light microscopy (paraffin sections) and by light microscopic review of "thick" sections, but not using electron microscopy - 88305 and 88313.

4. A lung wedge biopsy studied by light microscopy (paraffin sections), electron microscopy and immunoperoxidase staining - 88307, 88348 and 88342.

5. A muscle biopsy studied by light microscopy (paraffin sections) and electron microscopy - 88305 and 88348, or 88305, 88313, and 88348.

6. A lung wedge biopsy studied by light microscopy (paraffin sections) and scanning electron microscopy with EDX - 88307 and 883497.

7. Fluid from a blister negatively stained with uranyl acetate and examined by CTEM - 88348.

8. A sample of several individual hairs from a child with a genetic abnormality studied by scanning electron microscopy only - 88349.

This short essay on CPT coding is included  in order to encourage discussion on this topic.  Your comments/criticisms/suggestions are welcome and needed.    Please send your comments to or