The role of estrogen receptor alpha (ER alpha) and estrogen receptor beta (ER beta) gene polymorphisms on semen quality is the aim of our study. One hundred fourteen men were examined in the In Vitro Fertilization Unit of Ioannina Medical School, and it was found that 85 men had normal sperm count and 29 were oligozoospermic. The genotype analysis, on DNA extracted from spermatozoa, revealed that in men with oligozoospermia (sperm concentration <20 x 10(6) spermatozoa/mL), those with ER alpha 397T/C and 397C/C genotypes had higher sperm motility whereas those with 397T/T genotype had lower sperm motility (P = .003). In addition, men with ER alpha 351A/A genotype had lower sperm motility compared with 351A/G and 351 G/G genotypes (P = .013). Furthermore, normal-sperm-count men with ER alpha 397T/T genotype had higher sperm concentration compared with 397T/C and 397C/C genotypes (P = .016), whereas men with ER alpha 351A/A genotype had higher sperm concentration than those with 351A/G and 351G/G genotypes (P = .05). In contrast, no significant associations were found between ER beta (1082G-->A and 1730A-->G) polymorphisms and sperm concentration or motility. In conclusion, ER alpha polymorphisms were found to be associated with sperm motility and concentration. supporting the significance of this gene in spermatogenesis and semen quality.