BACKGROUND Annual chlamydia screening is recommended for all sexually active women aged <25 years. Substantial limitations exist in ascertaining chlamydia trends. Reported case rates have increased likely due to increased screening and improved test technology. Other data suggest that prevalence has decreased. METHODS Data from the Infertility Prevention Project (IPP), a national chlamydia screening program, were used to assess trends in chlamydia positivity from 2004 to 2008 among women aged 15 to 24 years who were tested in family planning clinics reporting data to IPP. Using the clinic as the unit of analysis, a correlated, longitudinal data analysis with a random intercept was conducted among clinics reporting ≥3 years of data during the analysis timeframe. Sensitivity analyses were performed to address the impact of various clinic participation levels in addition to the assessment of various correlation structures. RESULTS Over 5 million chlamydia tests were reported to IPP family planning clinics from 2004 to 2008. A majority of tests were conducted among white women (clinic-specific mean: 63.2%, interquartile range: 37.6%-91.5%); the clinic-specific mean percent of tests conducted among black women was 17.9% (interquartile range: 0.8%-25.7%). Overall chlamydia positivity from 2004 to 2008 was 7.0%. The odds ratio associated with a single year change (1.00; 95% confidence interval: 0.99, 1.00) suggested that chlamydia positivity did not change from 2004 to 2008, after controlling for clinic-specific population factors (age, race, test usage, and geography). CONCLUSIONS Findings support previous analyses suggesting that chlamydia prevalence is not increasing despite apparent increasing rates based on case reports.