The natural course of Chlamydia trachomatis infection and its risk factors were studied in Colombian women with normal cytological results, during a 5-year period. Eighty-two women who were found to be positive for C. trachomatis at the start of the study were studied at 6-month intervals. At each visit, a cervical scrape sample was obtained for detection of C. trachomatis by use of C. trachomatis endogenous-plasmid polymerase chain reaction (PCR)-enzyme immunoassay and VD2-PCR-reverse line blot assay. Of the women studied, 67% had a single-serovar infection, 10% had a mixed-serovar infection, and 23% had an infection with an unidentified type. An inversed rate of clearance of C. trachomatis infection was observed with oral contraceptive use (hazard ratio [HR], 1.7 [95% confidence interval {CI}, 1.1-2.7]) and first sexual intercourse at >/=20 years of age (HR, 4.3 [95% CI, 2.3-8.0]). Serovars of group B (B, D, and E) and C (H, I, J, and K) had a decreased rate of clearance (rate ratio, 0.4 [95% CI, 0.1-0.9]), compared with that for serovars of the intermediate group (F and G). At 4 years of follow-up, 94% of the women had cleared their infections.