A single-tube nested PCR able to discriminate between ocular infection with Chlamydia trachomatis of serovar A, B, or C is described. The method uses genotype-specific primers labeled with different fluorochromes, "drop-in/drop-out" PCR amplification, and product analysis on an Applied Biosystems 373A DNA Sequencer using GENESCAN 672 software. The system readily detected mixed infection with serotypes A and B within the same eye. This strategy provides a rapid genotyping method applicable to a wide variety of epidemiological studies.