Objective To explore the association between rs4705342 and rs4705343 polymorphisms in the flanking region of miR-143/145 and risk of bladder cancer. Methods A hospital-based case-control study was performed. Peripheral venous blood samples were taken from 106 patients with bladder cancer and 162 control individuals. The rs4705342 polymorphism was genotyped using TaqMan assay and the rs4705343 polymorphism was genotyped using polymerase chain reaction-restriction fragment length polymorphism. Results The rs4705342CC genotype and C allele were associated with a decreased risk of bladder cancer(CC vs. TT: adjusted OR=0.30,95%CI: 0.10-0.88,P=0.018;C vs. T: adjusted OR=0.60,95%CI:0.40-0.89,P=0.01). Haplotype analysis showed that rs4705342C-rs4705343T haplotype was associated with a decreased risk of bladder cancer compared with the rs4705342T-rs4705343T haplotype (OR=0.33,95%CI:0.15-0.74). Conclusions The rs4705342CC genotype in the flanking region of miR-143/145 may protect against the development of bladder cancer.