Chlamydia trachomatis (CT), the most prevalent sexually transmitted infection in the United States, disproportionately infects women and people of color. This study aimed to identify risk factors for racial and ethnic disparities for CT infection, re-infection, and persistent infection among pregnant women. We present a secondary analysis of births from a retrospective cohort study in Syracuse, NY from January 2000 through March 2002. African American women [OR 3.35 CI (2.29, 4.92)], Latin American women [OR 4.35 CI (2.52, 7.48)], unmarried women [OR 7.57 CI (4.38, 13.10)], and teen mothers [OR 3.87 CI (2.91, 5.16)] demonstrated statistically significant increased risk for infection. In multivariate analyses that included male partner variables, father's race/ethnicity but not the mother's race/ethnicity remained statistically associated with CT. Despite near universal rates of screening pregnant women, challenges to CT control remain and reflect barriers to testing and treatment of male partners.