This study investigated gene abnormalities in bladder cancer patients and the relationship between chromosomal alteration and the clinical outcome using microsatellite analysis. A total of 45 human bladder tumor patients were analyzed. The microsatellite markers for 18q21.1 (D18S46, D18S363, and D18S474), 9p21-22 (D9S171, D9S747, D9S1747, and IFNA), and 17p13.1 (TP53) were used for the loss of heterozygosity (LOH) detection. The clinical outcomes were estimated with univariate and multivariate analyses. The results show that patients with LOHs in 18q21.1 and 9p21-22 exhibited a significantly poor prognosis. LOHs of these chromosomal regions had the most predictable potential compared with the other known prognostic factors, such as tumor grade, TNM stage, and age. It is concluded that microsatellite analysis for 18q21.1 and 9p21-22 is capable of predicting the clinical outcome of bladder cancer patients.