The chromogranin/secretogranin (Cg/Sg) molecules are a family of acidic proteins present in neuroendocrine cells and tumors with secretory granules. They have been frequently used to characterize neuroendocrine cells and tumors by immunohistochemical analyses. Immunoreactivity for CgA is related to the presence of secretory granules in these tumors, so immunohistochemical staining for CgA may be absent in neuroendocrine tumors with only a few secretory granules. RNA in situ hybridization with a series of oligonucleotide probes for CgA and CgB was used to detect the mRNA transcripts for CgA and CgB with digoxigenin-labeled probes in 31 neuroendocrine tumors. These results were compared to ISH with 35S-labeled probes and with immunohistochemical staining for CgA and synaptophysin in the same neoplasms. ISH with 35S-labeled probes for CgA and B detected mRNA transcripts in 31 of 31 tumors, whereas the digoxigenin-labeled probe cocktails for CgA and B were positive in 19 of 31 cases when used separately and in 24 of 31 cases when used together. Immunohistochemical staining for CgA was positive in 22 of 31 cases and for synaptophysin in 23 of 31 cases. The CgA and B oligonucleotide probe cocktails were highly specific, since nonneuroendocrine cells and tumors did not stain and the hybridization signal was abolished by ribonuclease A pretreatment. These results indicate that non-isotopic ISH with digoxigenin-labeled probe cocktails for CgA and B or with 35S-labeled probes can be used in characterizing neuroendocrine cells and tumors in formalin-fixed paraffin-embedded tissue sections even when the CgA protein is not detected by immunohistochemistry.