Objective To investigate the possibility of microsatellite alteration (MA) in diagnosis of bladder cancer of Chinese people, and find the better panel which will be used in clinic. Methods A total of 6 and 10 microsatellite markers were chosen, PCR-SSLP silver staining assay was performed in 31 and 32 bladder cancers tissue, exfoliate cells in urine and 10, 15 non-bladder cancers exfoliate cells in urine, respectively. Results MA(+) was found in 28 out of 31, 30 out of 32 bladder cancers, and the sensitivity was 90.3%, 93.7% respectively. The MA of urine sediment of 25 non-bladder cancers was negative, and the specificity was 100%. The cytology was carried out among 19 out of 31, 20 out of 32 bladder cancers at the same time, 2 cases (10.3%) and 3 cases (15%) were found cancer positive, and the sensitivity is significantly lower than that by the analysis of MA in exfoliated cells. Conclusion MA was not associated with grade and stage of the bladder cancer. MA assay is a sensitive and effective method for the early detection of bladder cancer and post-operation surveillance.