OBJECTIVE: To study the relationship between self-rated health (SRH) and semen quality. DESIGN: Cross-sectional study of men attending a compulsory physical examination to determine their fitness for military service from 1996 to 2005. SETTING: Young men were approached when they were summoned for a compulsory physical examination to determine their fitness for military service in two major Danish cities. PATIENT(S): A total of 3,457 Danish young men delivered a semen sample, had a physical examination performed, and responded to a questionnaire including a question about SRH. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Semen quality and testis size. RESULT(S): After control for confounders, men with good and poor SRH had, respectively, 0.5 mL (95% CI: -0.8, -0.1) and 0.8 mL (95% CI: -2.4, 0.8) smaller testes size compared to men with very good SRH, the trend was statistically significant. Men with good and poor SRH had, respectively, 12.2% (95% CI: -21.2%, -2.2%) and 26.9% (95% CI: -55.7%, 20.8%) lower total sperm count compared to men with very good SRH, the trend was statistically significant, and had +0.4% (-1.4%, 2.2%) and 1.4% (-3.5%, 0.7%) fewer morphologically normal sperms (trend statistically significant). Percentages of motile spermatozoa and semen volume were not significantly associated with SRH. CONCLUSION(S): We found significant associations between SRH and semen quality and testicular size. Given the cross-sectional study design, we cannot establish a causal relationship but argue that SRH may be associated with semen quality. Our findings need to be validated and confirmed with other study designs (preferably prospective) and in populations of different age structure and fertility status.