OBJECTIVE: To study the association between use of protein supplements (PS) and semen quality among young men. DESIGN: Cross-sectional study. SETTING: Not applicable PATIENT(S): We used data from the Fetal Programming of Semen Quality (FEPOS) cohort, which is a subsample of 778 men whose mothers enrolled in the Danish National Birth Cohort 1996-2002. INTERVENTION(S): Semen samples were collected from April 2017 to March 2019. Relative difference in semen characteristics according to self-reported PS use was estimated with negative binomial regression adjusting for lifestyle factors including exercise, body mass index, and use of anabolic steroids, and maternal and paternal factors potentially confounding the association between PS and semen quality. MAIN OUTCOME MEASURE(S): Negative binomial regression yielded the best fit and was used to estimate the percent difference with 95% confidence intervals in semen volume, sperm concentration, total sperm count, proportions of progressive, nonprogressive, and immotile sperm, and percentage of morphologically normal sperm in former and current users of PS relative to never users. RESULT(S): PS was used currently by 28% and formerly by 24% of participants. PS use was not associated with reduced semen quality in terms of semen volume, sperm concentration, total sperm count, morphology, or motility in either crude or adjusted analyses. CONCLUSION: This study showed no association between use of PS and semen quality characteristics. Still, we encourage others to repeat the study, as even a small harmful effect would have a large impact on the population level because of the widespread use of PS among young men.