The S100 proteins act as multifactional signaling factors that are involved in the regulation of diverse cellular processes. To explore the involvement of S100 genes in bladder cancers, S100 gene expressions were systematically evaluated at the RNA level by microarray and real-time PCR. Total RNAs were obtained from 4-hydroxybutyl(butyl)nitrosamine (OH-BBN)-induced mouse and rat bladder cancers, human bladder cancers and matched normal bladder urothelium. Microarray analysis was performed on mouse and rat bladder cancers; real-time PCR was performed in mouse, rat and human bladder cancers and their matched normal urothelium for confirmation. Microarray analysis revealed that 9 and 6 members of the S100 gene family were differentially expressed in mouse and rat bladder cancers, respectively. Thirteen members of the S100 gene family were confirmed by real-time PCR to be differentially expressed in human bladder cancers, with overexpression of S100A2, S100A3, S100A5, S100A7, S100A8, S100A9, S100A14, S100A15, S100A16 and S100P, and underexpression of S100A1, S100A4 and S100B. S100A1, S10OA3, S100A8, S10A9, S100A14, S100A15 and S100A16 showed similar patterns of differential expression in bladder cancers from mouse, rat and human. To our knowledge this is the first report of systematic evaluation of S100 gene expressions in bladder cancers. Our results indicate that differential expression of S100 gene family members is characteristic of bladder cancers and these genes may play important roles in bladder tumorigenesis and progression.