Androgens, including 5alpha-dihydrotestosterone (DHT), are known to play a role for spermatogenesis and accessory sex gland function. The enzyme 5alpha-reductase (SRD5A) catalyses the conversion of testosterone to DHT. Our objective was to investigate whether polymorphisms in the SRD5A2 gene influence semen parameters in the general population. DNA from 182 Swedish military conscripts was examined for the A49T, V89L, and R227Q polymorphisms in the SRD5A type 2 gene. Ejaculates were analysed according to WHO guidelines. In addition, sperm motility was assessed using computer-aided sperm analysis (CASA). Seminal markers of epididymal (neutral alpha-glucosidase), prostatic (prostate specific-antigen and zinc), and seminal vesicles function (fructose) were measured. The A49TT-allele was associated with significantly higher sperm concentration compared with the wild type A-allele (mean: 102 x 10(6)/mL vs. 57 x 10(6)/mL, p = 0.02). The V89LV-genotype was correlated with significantly higher proportion progressive motile spermatozoa compared with the L-variant (mean: 55% vs. 48%, p = 0.04). The same trend was found regarding the CASA motile spermatozoa (mean: 52% vs. 41%, p = 0.02). No association between any of the polymorphisms and biochemical markers was found. SRD5A2 gene variants were associated with sperm concentration and motility, but not with epididymal and accessory sex gland markers. This effect on sperm parameters might therefore be exerted via a direct effect of DHT on spermatogenesis.