Muir-Torre syndrome (MTS) is characterized by the presence of at least one sebaceous tumor and at least one visceral malignancy. Although a wide range of internal malignancies have been reported, the most frequently observed internal neoplasm is colorectal carcinoma. MTS and hereditary nonpolyposis colorectal carcinoma (HNPCC) share many clinical and pathological characteristics and thus may share similar genetic mechanisms of tumorigenesis. Recently, microsatellite instability (MIN) has been reported in tumor tissue from patients with HNPCC. In order to determine if tumors from MTS patients might also show MIN, we examined DNA extracted from paraffin-embedded tissues for the presence of MIN at (CA)n repeats on chromosomes 5q, 15q, 17p, and 18q. Data was obtained on 13 patients, 9 of which had at least one colorectal tumor. Of these, six demonstrated widespread MIN in all sebaceous and colorectal tumors examined, as well as in a transitional cell carcinoma of the renal pelvis, a prostatic adenocarcinoma and a keratoacanthoma. Overall, patients with MIN differed from patients without MIN in several respects, the most important of which include: (a) uniform presence and early onset of colorectal cancer (average age, 40 versus 70 years); (b) prolonged survival following diagnosis of visceral malignancy (median survival, 32 versus 11 years); and (c) a greater number of visceral and skin tumors. These data suggests that patients with MTS may be composed of at least two subgroups, each demonstrating different genetic, pathological and clinical features. Furthermore, the subgroup demonstrating MIN may share similar genetic mechanisms of tumorigenesis with patients having HNPCC, supporting the notion that these syndromes are allelic.