Chlamydia trachomatis (CT) is a common sexually transmitted infection for which young, sexually active persons are at highest risk. Health consequences such as orchitis/epididymitis, prostatitis, infertility, and urethral stricture have been described among CT-infected males, although not all of these are indisputably linked to CT. Current literature lacks population-based studies needed to examine these associations on a larger scale, to evaluate the true risk of developing complications after a CT infection. The US Air Force contains a large population of young, sexually active males, making it suitable for conducting such a study. We conducted a retrospective cohort study between 2001 and 2005 comparing the incidence of orchitis/epididymitis, prostatitis, infertility, and urethral stricture among male Air Force members with and without prior CT infections. Cumulative incidence rates were calculated and Cox proportional hazard models were generated to evaluate the risk of developing complications and to adjust for potential confounders. Among 17,764 men enrolled in the study, 913 (5.14%) experienced a reproductive tract outcome. Among CT-positive men, cumulative incidences of orchitis/epididymitis, prostatitis, infertility, and urethral stricture were 4.28%, 1.41%, 1.27%, and 0.13%, respectively. Orchitis/epididymitis [Hazard ratio (HR) = 1.38 (1.13-1.70)] and "any" outcome [HR = 1.37 (1.16-1.61)] were positively associated with CT; infertility was marginally associated [HR = 1.36 (0.93-2.00)]. Overall, the burden of reproductive health outcomes among Air Force males is small. Significant associations were observed between CT and both orchitis/epididymitis and any outcome; a larger cohort or longer follow-up may have detected a significant association between CT and infertility.