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Annual chlamydia (CT) screening is recommended for women younger than 25 years, yet less than half of young women seeking health care are screened annually. We analyzed Title X family planning service data from the Northwest United States to assess factors associated with missed opportunities for CT screening. Our primary hypothesis was screening coverage is higher during annual preventive health visits compared to other visit types. Study objectives were: (1) identify gaps in screening coverage by patient demographics, visit characteristics, and clinic measures; and (2) examine the association between visit type and CT screening by controlling for other covariates and stratifying by state.Calendar year 2011 Title X visit records (n = 180,856) were aggregated to the patient level (n = 112,926) to assess CT screening coverage by all characteristics. Screening variation was explored by bivariate and multivariate Poisson regression. Adjusted models for each state estimated association between comprehensive examination and screening controlling for confounders.Clinic and visit characteristics were associated with CT screening. Coverage ranged from 45% in Washington to 80% in Alaska. Only 34% of patients visited for a routine comprehensive examination. Visit type was associated with screening; 75% of patients who had a comprehensive examination were screened versus 34% of those without a comprehensive examination (unadjusted PR, 2.18; 95% confidence interval, 2.16–2.21). The association between comprehensive examination and CT screening varied significantly by state (interaction term, P < 0.001).Missed screening opportunities are common among women who access brief appointments for specific needs but do not seek routine preventive care, particularly in some states. Structural interventions may help address these systematically missed opportunities.