Background Reporting systems are commonly used for chlamydia and gonorrhea surveillance and community burden assessments. Estimates are conservative given high proportions of asymptomatic cases and underreporting. The military's unified health system, which includes laboratory and medical encounter data, could offer insight into surveillance gaps and improve burden analyses. Methods Confirmed chlamydia and gonorrhea cases reported among active component soldiers were merged with laboratory and medical encounter records indicative of infection to identify incident cases during 2015-2019. Case capture across data systems was assessed, and reported case rates were compared with those derived from the enhanced 3-source database. Attributable medical encounters for total cases were extrapolated using average visits for the subset of cases with supporting encounter data. Multivariable generalized linear models were generated to characterize infections. Results Approximately 83% and 76% of respective chlamydia and gonorrhea cases were identified through reporting, compared with 87% and 67% through laboratory records, and 58% for both through medical encounters. Rates from enhanced 3-source surveillance peaked at 2844 chlamydia and 517 gonorrhea cases per 100,000 person-years in 2019, reflecting 17% and 28% increases in respective rates compared with reported rates. Overall, 3163 cases of chlamydia and/or gonorrhea per 100,000 person-years were detected in 2019, affecting 13,004 soldiers and requiring an estimated 21,690 medical encounters. Soldiers who were younger, female, racial/ethnic minorities, nonmarried, enlisted, less educated, and Southern residents had significantly higher risk. Conclusion Integration of laboratory and medical encounter data substantially improved burden estimation over reporting alone. Rates generated remain conservative because they only reflect documented cases. Increasing rates support prevention prioritization, particularly among young soldiers.