The aim of this study was to investigate STK15 amplification in histologically benign urothelium and invasive tumor tissue of urothelial bladder cancer patients in relation to clinicopathologic and molecular characteristics, and to analyze a hypothesized association between the STK15 single nucleotide polymorphism at site T91A (Phe31Ile) and STK15 gene amplification. A tissue microarray (TMA) was constructed and contained formalin-fixed paraffin-embedded tumor tissue and matching histologically benign urothelium of 44 patients who underwent cystectomy for invasive urothelial carcinoma. Expression of TP53, CK20 and MIB1 was evaluated by immunohistochemistry. UroVysion and STK15 fluorescence in situ hybridization (FISH) analysis was performed for sensitive detection of polysomy, relative p16 deletion and STK15 amplification, respectively. Genotypes of STK15 at the T91A (Phe31Ile) site were analyzed by PCR-RFLP assay. Low level STK15 amplification was found in 2 of 36 analyzable histologically benign urothelium specimens (5.6%) and in 64% (28/44) of urothelial bladder cancers, whereas 36% (16/44) of cancer lesions showed high level of STK15 amplification. In histologically benign urothelium of bladder cancer patients, low level STK15 amplification was associated with shorter recurrence-free and tumor-specific survival. There was no correlation between allelic variants and high/low level of STK15 gene amplification. Applying STK15 FISH to benign urothelium of bladder cancer patients may help to identify patients at increased risk for adverse clinical outcome. A large randomized prospective study comparing early versus delayed cystectomy in patients with pT1 bladder cancer is currently conducted to validate our findings.