In humans, guanylyl cyclase C (GCC) is expressed by mucosal cells lining the intestine, from the duodenum to the rectum, but not by extraintestinal tissues. Expression of GCC persists after mucosal cells undergo neoplastic transformation, and this protein has been identified in all primary and metastatic colorectal tumors examined to date, suggesting that GCC may be a highly specific biomarker for colorectal cancer. The utility of GCC as a diagnostic biomarker and therapeutic target is predicated, in part, on defining the variability of its expression in colorectal cancer cells. Similarly, the utility of this biomarker to define tumor burden in diagnosing, staging, and postoperative surveillance of patients is predicated on quantifying GCC expression in cancer cells in tissues and blood. The present studies examined the heterogeneity of GCC expression in eight human colorectal carcinoma cell lines in vitro representing the full spectrum of cytological differentiation. Quantification of GCC expression by ligand binding and stimulation of cGMP accumulation demonstrated that functional GCC expression is heterogeneous in different colorectal cancer cell lines. Qualitative reverse transcription (RT)-PCR demonstrated that all colorectal cancer cells examined expressed GCC mRNA. However, GCC expression varied 100-fold in different colorectal cancer cell lines, determined by a novel quantitative RT-PCR assay. Functional and molecular expressions of GCC were unrelated to the differentiation state of cancer cells. These studies suggest that GCC is heterogeneously expressed by colorectal cancer cells in vitro and suggest a role for quantitative RT-PCR analysis in the development of diagnostic tests using GCC as a biomarker for metastatic colorectal cancer.