BACKGROUND: Trachoma is the leading infectious cause of blindness. Routes of transmission remain unclear. In this study, the relationship between Chlamydia trachomatis Amplicor-positive nasal discharge and Amplicor-positive ocular swabs was investigated (Amplicor; Roche, Indianapolis, IN). METHODS: A longitudinal study was conducted in Tanzania and The Gambia. Eyes were graded for active trachoma; ocular swabs were taken to test for C. trachomatis. Children with visible nasal discharge had swabs taken of this material. Participants were offered systemic antibiotics. Two months after treatment, participants were re-examined. RESULTS: Of the 1128 children participating, 188 (17%) had nasal discharge. Among 188 children with nasal discharge, 64 (34%) nasal swabs were PCR positive. There was a strong correlation between active disease/ocular chlamydial positivity and positive nasal discharge. Children with Amplicor-positive ocular swabs were 9.9 times more likely to have Amplicor-positive nasal discharge than were children without ocular positivity (95% CI: 4.34-22.53). Two months after treatment, 16% had an Amplicor-positive ocular swab. Children with positive nasal discharge at baseline were 5.2 times more likely to have an Amplicor-positive ocular swab at 2 months than were children without Amplicor-positive nasal discharge at baseline (95% CI: 1.54-17.23), after adjusting for baseline ocular positivity, gender, and study site. CONCLUSIONS: Nasal discharge may provide a source of reinfection with C. trachomatis, after antibiotic treatment for trachoma, either through transfer of secretions from nose to eye or from nasal secretions transferred to bed sheets or dirty clothes and back to the eye; alternatively, nasal discharge may be an indicator of severe persistent ocular chlamydial infection that is not cleared with a single dose of antibiotics.