Cyclophosphamide (CP) causes extensive cystitis, which is ameliorated with concomitant treatment with mesna. We investigated the protective mechanisms of mesna in the expression of uroplakin (UP), a strong mucosal barrier against toxic materials, in CP-induced rat cystitis. A total of 54 SD female rats received a single intraperitoneal injection of 200 mg of CP/kg. Six CP-treated, 6 CP + mesna (120 mg/kg)-treated rats, and 6 negative controls were sequentially sacrificed at 12, 24, and 72 h post-CP injection. The bladders were harvested. The levels of UPIa, Ib, II, and III mRNA on real-time PCR, the UPII and III expressions on immunoblotting, and the UPII expression on immunolocalization study in the harvested bladder were maximally suppressed within 12-24 h, whereas partially or completely recovered at 24-72 h post-CP injection. In addition, the responses in UPs after a CP insult were heterogeneous (i.e., markedly suppressed in UPII and lesser destructive in UPIII). Even though the mesna-treated rats also showed transient and small reductions in the mRNA levels of all UPs, mesna clearly preserved the UP expressions of mRNA and protein in CP-induced urinary bladder mucosa. In conclusion, this study suggests that CP transiently reduces the expression of UPs and mesna protects the urinary bladder mucosa through the preservation of UPs protein.