BACKGROUND We investigated the androgen receptor gene GGN polymorphism and its relation to male infertility and receptor function. METHODS Ninety-nine infertile patients with sperm counts < or = 5 x 10(6)/ml were screened for karyotypic abnormalities and Y-chromosome microdeletions. The GGN and CAG repeats were sequenced in those without genetic abnormalities and in 223 controls. RESULTS Five men (5.1%) carried Y-chromosome microdeletions and five had abnormal karyotypes. Neither the distributions of GGN nor of CAG differed significantly between patients and controls. However, the < 21 CAG and GGN = 23 combination of repeats occurred more frequently in the controls (16%) compared to the entire group of patients (4%; P = 0.003) and to the subgroup of 54 patients with idiopathic infertility (4%; P = 0.02). Testicular volume and CAG lengths were higher (P = 0.04 and 0.002 respectively) among the patients with GGN = 23 compared to GGN = 24. The odds ratio (OR) of having low prostatic secretory function was higher among patients with GGN = 24 than those with GGN = 23 (OR: 3.5; 95% CI: 1.1-11.7; P = 0.04). CONCLUSIONS The < 21 CAG and GGN = 23 combination of repeats may confer a lower risk of infertility to the carriers. Androgen sensitivity may be higher among carriers of the GGN = 23 allele compared to the GGN = 24 allele.