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Objective: To apply urine-based ligase chain reaction for Chlamydia trachomatis (C. trachomatis) and Neisseria gonorrhoeae (N. gonorrhoeae) detection and standard urine-based pregnancy testing for Navy-enlisted women, and to compare the prevalence and epidemiologic correlates of these adverse reproductive outcomes., Methods: Participants were surveyed and urine was collected for pregnancy testing using standard laboratory methods and detection of C. trachomatis and N. gonorrhoeae infection by ligase chain reaction. Self-administered surveys facilitated collection of demographics, sexual behavior, including contraceptive use, sexual partners, sexually transmitted disease, and pregnancy history., Results: Among 299 of 314 participants, the prevalence of chlamydial infection was 4.7% and of pregnancy was 9.7%, with 48.3% of the pregnancies unplanned. Chlamydia trachomatis infection was univariately associated with having a new sex partner within the last 6 months, more sexual partners, single marital status, condom use, drinking until passing out or vomiting in the past 30 days (alcohol misuse), and current pregnancy. Unplanned pregnancy was univariately associated with young age, single marital status, inconsistent condom use, having a new sex partner within the last 6 months, and more recent sexual partners. Among the pregnant women, four (13.8%) were infected with C. trachomatis., Conclusion: The high rates of chlamydial infection and unplanned pregnancy found in this population of employed young women with ready access to health care and health education underscore the challenge of enhancing reproductive health via compliance with effective contraceptive and sexually transmitted disease prevention methods. This is a challenge that remains unmet.