Immunohistochemical stains are occasionally performed on paraffin-embedded, fixed material that was previously frozen, most frequently for an intraoperative frozen section diagnosis. A retrospective study comparing immunohistochemistry on previously frozen then fixed tissue with freshly fixed tissue was designed. Of 43 cases identified during the period 1994-1996 in which immunohistochemistry was performed on frozen section blocks, 19 met criteria for inclusion. Immunohistochemistry using antibodies to S-100, HMB-45, synaptophysin, chromogranin, neuron-specific enolase (NSE), neurofilament, glial fibrillary acidic protein, vimentin, and carcinoembryonic antigen (CEA) was compared. Staining for cytokeratins was unchanged. Staining for S-100, HMB-45, synaptophysin, and NSE were negative in frozen/fixed tissue and positive in comparable fresh/fixed tissue in at least one case each. Chromogranin and CEA exhibited a significant decrease in the frozen/fixed tissue. We conclude that caution must be exercised in interpreting immunohistochemical results using tissue that was frozen for intraoperative consultation before formalin fixation and paraffin embedding.