Cigarette smoking is quite prevalent in the general population but our knowledge of its effect on male reproductive function is still very limited. Therefore, we investigated the impact of tobacco exposure on reproductive characteristics in young males. Military conscripts, 217 non-smokers and 85 smokers, with a median age of 18 years were enrolled. Physical examination and semen analysis, including measurement of accessory sex gland markers and reproductive hormone levels, were performed. Lifestyle-associated factors, including maternal smoking during pregnancy and snuffing, were recorded. Non-smokers had 49% higher total sperm number than smokers (95% CI 4.5-112%, p = 0.01). In addition, sperm concentration was 37% higher among non-smokers (95% CI -4% to 95%, p = 0.08). Serum levels of follicle-stimulating hormone (FSH) were 17% higher among non-smokers (95% CI 3-33%, p = 0.02), whereas no significant differences between smokers and non-smokers were found for inhibin B, testosterone, sex hormone binding globulin, luteinizing hormone and oestradiol. Those who smoked >10 cigarettes per day exhibited 37% lower (95% CI 10-69%, p = 0.005) FSH levels than those who smoked less. Maternal smoking during pregnancy had a negative impact on epididymal and seminal vesicle marker secretion. Smoking seems to impair sperm production and epididymal as well as accessory sex gland function and could be one of the factors contributing to regional differences in sperm parameters.