BACKGROUND: Colorectal cancer has an important genetic component. Microsatellites are considered phenotypic markers of prognosis, therapeutic response and identify patients with mutations in DNA repair genes. AIM: To evaluate the molecular profile of tumors underwent to transanal endoscopic microsurgery-TEM in surgical treatment of rectal cancer. METHOD: Thirty eight surgical specimens were evaluated according to pathological staging and the region of the tumor were dissected and submitted to DNA extraction. The colorectal tumors were tested for microsatellite instability-MSI using a panel of five markers (BAT25, BAT26, D2S123, D5S346, and D17S2720) technique of Polymerase Chain Reaction (PCR). RESULT: From total 63% were male and 47% female, with mean age of 58.4 years. In relation to tumor type adenomas were 58%, 24% low-grade adenomas and 76% high grade; 42% were carcinomas. The depth of resection 80% included the rectal perirenal fat and 20% the muscularis propria. The most frequent microsatellite amplification was BAT26 (100%) and lowest D17S2720 (85.4%). Sixteen patients (42%) were MSI, ten were carcinomas, two low grade adenomas and four high grade. Twenty-two cases (68%) showed microsatellite stable-MSS. The allelic loss of microsatellite markers was statistically significant in cases of carcinoma in relation to adenomas. The most frequent microsatellite amplification was BAT26 (100%) and lower D17S2720 (85.4%), 16 patients (42%) had microsatellite instability-MSI thereof ten were carcinomas, two low grade adenomas, four high-grade adenomas and 22 cases (58%) were microsatellite stable-MSS. CONCLUSION: Microsatellite instability (MSI-H) was significantly associated with rectal carcinomas, confirming its use as a prognostic marker in colorectal carcinogenesis.