The H2BFWT (H2B family, member W, testis specific) gene is a testis-specific histone which is involved in the spermatogenesis process. This study aimed to investigate the association of H2BFWT gene c.-9C>T and c.368A>G polymorphisms with male infertility in an Iranian population. The 232 independent individuals, including 109 infertile men and 123 healthy controls, were recruited from IVF centre (Kashan, Iran). The allele types of c.-9C>T and c.368A>G polymorphisms were detected by using PCR-RFLP method. In overall analysis, we found that the c.-9T (OR: 1.75, 95% CI: 1.04–2.95, p = .035) and c.368G (OR: 1.71, 95% CI: 1.02–2.89, p = .042) alleles are associated with male infertility. The c.-9T allele was also associated with nonobstructive azoospermia (OR: 2.08, 95% CI: 1.01–4.25, p = .046), while c.368G allele was associated with oligozoospermia (OR: 2.10, 95% CI: 1.15–3.85, p = .016). It is concluded that H2BFWT gene c.-9C>T and c.368A>G polymorphisms might be genetic risk factors for idiopathic male infertility.