The effect of alcohol on spermatogenesis and morphometric analysis of the human testis was investigated in a prospective autopsy study, with detailed alcohol-use reports from relatives or friends of the deceased. The autopsy series comprised non-alcoholic controls (daily intake < 10 g; n = 32) and heavy-drinkers (n = 44) with an intake of > 80 g per day. Of the controls, 26 (81.3%) men showed normal spermatogenesis, and six (18.7%) partial spermatogenic arrest. Of the heavy drinkers, only 16 (36.4%) had normal spermatogenesis (p < 0.001), while 23 (52.3%) showed partial or complete spermatogenic arrest (p < 0.001) and five had Sertoli cell-only (SCO) syndrome (p < 0.05). The mean testicular weight of heavy-drinkers was slightly (p < 0.05) lower than in the controls. Compared to men with normal spermatogenesis, testicular weight was slightly lower both in controls and heavy-drinkers with spermatogenic arrest, and was significantly (p < 0.01) lower in heavy-drinking men with SCO syndrome. Spermatogenic arrest was not correlated with fatty liver or cirrhosis of the liver, whereas four of the five men with SCO syndrome exhibited a fatty liver. Thus, our results suggest that the most common alcohol-related pathological change in the testes is probably reversible arrest of spermatogenesis. Furthermore, we suggest that many heavy social drinkers may suffer from self-inflicted infertility, as one tenth of heavy-drinkers in our study had SCO syndrome.