In male mice heterozygous for a null apolipoprotein B (apoB), allele infertility was noticed. These data led us to investigate a possible role of APOB gene polymorphism and male infertility in humans. In this case-control study, we searched for an association between the insertion/deletion (I/D) polymorphism of the APOB gene and male infertility in 560 Slovene Caucasian men. The study group consisted of 310 infertile patients: 115 with azoospermia and 195 with oligoasthenoteratozoospermia (OAT) and a control group of 250 fertile men. We found a statistically significant difference in the genotype distribution between the two groups (chi2 = 6.315, P = 0.043). A separate analysis of azoospermic and OAT patients demonstrated that significant differences in genotype distribution were limited to the OAT group (chi2 = 7.011, P = 0.030). The presence of the D allele (DD or ID genotypes) conferred a 1.6 risk [chi2 = 6.089, P = 0.014, 95% confidence interval (95% CI) = 1.102-2.347] for male infertility in the OAT group of patients. We did not find a correlation between the I/D polymorphism genotypes and the clinical characteristics of infertile men: sperm concentration (P = 0.102), rapid progressive motility (P = 0.449), normal morphology (P = 0.085) and Johnsen score (P = 0.531). These data suggest that genetic variation in the signal peptide of the APOB gene (I/D polymorphism) might be a risk factor for the development of male infertility.