Possible altered gene expression patterns in bladder tumour carcinogenesis in rat bladder cancers induced by BBN [N-butyl-N-(4-hydroxybutyl)nitrosamine] was examined by cDNA microarray analysis of gene expression profiles. Thirty Sprague-Dawley rats were given drinking water containing 0.05% BBN ad libitum for 24 to 28 weeks. Equal numbers of control rats were given tap water without BBN. After treatment, the rat bladders were excised for RNA extraction and histopathological examinations. Total RNAs were extracted from rat transitional cell carcinoma (TCC) tissues and micro-dissected normal rat bladder epithelia. The atlas glass rat microarray was used, which included oligonucleotides of 1081 rat genes. Some of the up-regulated genes in rat bladder TCCs were further confirmed by Northern blotting. Our results showed that the transcriptions of 30 genes were significantly elevated in the rat bladder TCCs, and these included fly proto-oncogene, Lipocortin 2, COX IV, COX V a, and cathepsin D. Also, 15 genes were significantly down-regulated in the rat bladder TCCs and they included B7.1, TNFr1, APOA1 and VHL. The results of cDNA microarray analysis demonstrated that normal rat bladder epithelia and bladder TCC exhibited different and specific gene statement profiles. The increased expressions of the identified genes may play an important role in the chemically induced bladder carcinogenesis.