A total of 113 female commercial sex workers had individual alleles for HLA class II genes determined by using labeled sequence-specific oligonucleotide probes to hybridize to polymerase chain reaction products of amplified DNA. Women also had microimmunofluorescent (MIF) antibody titers to Chlamydia trachomatis elementary bodies and ELISA antibody to recombinant chlamydial heat-shock protein 60 (Chsp60) determined. Women were prospectively followed at monthly intervals over 2 years for incident C. trachomatis infection and acute pelvic inflammatory disease (PID). HLA DQA1*0401 and DQB1*0402 alleles were statistically associated with increased prevalence and amount of antibody to Chsp60 but not MIF antibody. However, these alleles did not alter the risk for chlamydial PID. The potential role that HLA DQ may play in chlamydial disease pathogenesis requires further study.