Bladder cancer is the ninth most common cancer in the world. Urothelial carcinoma (formerly known as transitional cell carcinoma) comprises the majority of bladder cancers. In order to decipher the genetic alteration leading to the carcinogenesis of urothelial cancer, we performed genome-wide allelotyping analysis using 384 microsatellite markers spanning 22 autosomes together with comparative genomic hybridization (CGH) in 21 urothelial cancer. High frequency of allelic imbalance was observed in chromosome arm 1q (61.9%), 3p (61.9%), 4q (66.67%), 8p (57.14%), 9p (76.2%) and 9q (66.67%). Allelic imbalance with frequency above average was also observed in chromosome arm 2q, 10p, 10q, 11p, 11q, 12q, 13q, 15q, 17p and 19q. The allelic imbalance of each case and fractional allelic loss for each chromosome was associated with higher tumor grade and stage (P<0.05). We have also delineated several minimal deletion regions on chromosome 3p, 4q, 8p, 9p, 9q, 11p, 13q, 16q and 17p. By CGH analysis, common chromosomal alterations included gain of 1p, 1q, 12q, 16p, 17q and 19p as well as loss of 4q and 9p in most of the cases. Our findings may provide valuable information to locate putative oncogenes and tumor suppressor genes in the carcinogenesis of bladder cancer in this locality.