Abstract: Objective To compare immunohistochemistry(IHC) with polymerase chain reaction(PCR) in evaluating the microsatallite instability(MSI) in colorectal carcinoma. Methods We used IHC and PCR to detect MSI status in 80 cases of colorectal carcinoma. Results (1) All cases exhibited mismatch repair protein(including MLH1, PMS2, MSH2 and MSH6) positive expression in the matched normal mucosas. The loss expression rates of MLH1, PMS2, MSH2 and MSH6 were 23.8%(19/80), 21.2%(17/80), 7.5%(6/80) and 3.7%(3/80). Both MLH1 and PMS2 expression deletion were found in 16 cases, and both MSH2 and MSH6 expression deletion were found in 3 cases. Immunohistochemisry results showed 19 cases were microsatallite instability-high(MSI-H), and the other were microsatallite instability-low/microsatallite stability(MSI-L/MSS); (2) PCR results showed there were 18 cases of MSI-H, 5 MSI-L and the remaining were MSS; (3) The results of IHC were accorded with PCR results. Conclusion Compared with PCR, IHC method is of simple operation, short cycle time, low cost and low requirement for experimental instruments. As a result, IHC is a preferred method in detecting MSI of colorectal cancer.