Cytochrome P4501A1 (CYP1A1) is a key enzyme in phase I bioactivation of polycyclic aromatic hydrocarbons (PAHs), which have potential reproductive toxicity. The aim of this study was to investigate the association of the CYP1A1 polymorphisms with male infertility in a Han-Chinese population. We genotyped two polymorphisms, CYP1A1*2A and CYP1A1*2C, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay in a hospital-based case-control study including 192 infertile patients with non-obstructive azoospermia or severe oligozoospermia and 226 fertile controls. We found that the genotype distribution of CYP1A1*2C was significantly different between the patients and the controls (p = 0.019). Analysis showed that CYP1A1*2C AG genotype was associated with a significantly decreased risk of male infertility [odds ratio (OR) = 0.56, 95% confidence interval (95% CI) = 0.36-0.86, p = 0.005] compared with the AA genotype. A statistically significantly decreased risk of male infertility was found to be associated with the CYP1A1*2C AG genotype plus GG genotype compared with CYP1A1*2C AA genotype (OR = 0.60, 95% CI = 0.40-0.91, p = 0.011). No significant association was detected between CYP1A1*2A polymorphism and male infertility. Haplotypic analysis showed a significantly increased risk of male infertility associated with the C-A haplotype compared with the T-A haplotype (OR = 1.98, 95% CI = 1.27-3.09), indicating a synergic effect of the two polymorphisms. Our results suggest that the CYP1A1 polymorphisms may contribute to the pathogenesis of male infertility in the Han-Chinese population.