Background: Testicular microlithiasis (TM) is sometimes found on scrotal ultrasound. The prevalence seems higher in populations of men with testicular dysfunction, and TM may be a risk factor for testicular germ cell neoplasia in situ in men with additional risk factors. The association between TM and testicular function is controversial, especially in incidentally found TM. Objectives: To determine the frequency of TM in young men from the general population, and associations between TM, semen quality, and reproductive hormones. Materials and methods: A cross-sectional study of 4850 Danish men, median age 19 years. Testicular pattern, including the presence of TM, was assessed by ultrasound examination. Participants provided a questionnaire, one semen sample, and one blood sample. Semen variables and serum reproductive hormones were analyzed as outcomes using multivariable regression analysis to determine associations with TM. Results: TM was detected in 53 men (1%), of which 19 (36%) were unilateral and 34 (64%) were bilateral cases. A history of cryptorchidism was associated with presence of TM. Bilateral TM was associated with slightly lower testicular volume, sperm concentration, and total sperm count. TM was not significantly associated with serum testosterone or other reproductive hormones. Discussion and Conclusion: TM is rare in men from the general population and is associated with lower sperm count if bilateral, although effect sizes were small. Current European guidelines do not recommend any follow-up in cases of TM with no other risk factors for testicular cancer. We suggest that men with incidentally found bilateral TM may be offered a semen analysis, but analysis of reproductive hormones seems unnecessary.