Polymerase chain reaction (PCR) with primers derived from the sequence of the cryptic chlamydial plasmid was evaluated for the detection of ocular chlamydial infection in trachoma-endemic populations and was used to explore further the relationship between ocular chlamydial infection and clinical signs of trachoma. It was more sensitive than other laboratory techniques, especially for mild cases of trachoma, in detecting infection in 144 (72%) of 200 who fulfilled the World Health Organization case definition. Of 1132 subjects who did not fulfill these criteria, 85 (7.5%) were PCR-positive, but about one-third of these 85 subjects had minor signs of trachoma. Clinically negative subjects who were PCR-positive were more likely than PCR-negative subjects to have acquired signs of disease at 1 and 6 months of follow-up. Clinical signs were twice as likely to have resolved after 1 month in PCR-negative subjects with disease than in those who were PCR-positive.