Recent prospective studies of male reproductive health have shown differences between several European countries. Our objective was to evaluate the current situation in the two Baltic States Estonia and Lithuania. In 1997–99 we investigated semen parameters, levels of reproductive hormones and general health factors of 196 men from the general population in Lithuania; from Estonia, 79 men from the general population and 118 soldiers were investigated. Adjusted for interlaboratory differences and abstinence period, sperm concentration of Lithuanian and Estonian men from the general populations were shown to be 55 and 67 million/mL, respectively. The Estonian soldiers had the highest sperm concentration, 82 million/mL. The frequencies of morphologically normal spermatozoa were 6.2, 7.7 and 9.6%, respectively. In contrast to the semen qualities, highest Inhibin B levels were detected in the Lithuanians (233 pg/mL) followed by Estonian men from the general population (220 pg/mL) and Estonian soldiers (185 pg/mL). The soldiers had also the lowest level of testosterone and oestradiol. The sperm counts of the Estonian and Lithuanian men investigated here are higher than recently shown for Norwegian, Danish, Estonian and Finnish men. Comparisons should be cautiously drawn as the groups are not completely comparable. Still, even within the Baltic region, geographically close and sharing common recent social history, differences in semen quality and levels of reproductive hormones are apparent.