We compared the ligase chain reaction (LCR) assay to cell culture for diagnosis of genitourinary chlamydial infections in women using swab specimens obtained by clinicians from the endocervix and by patients from their own vaginas. Specimens from 40 (12.9%) of 309 patients were positive for chlamydial infection by culture, while the specimens of 50 (16.2%) patients were positive by LCR. Chlamydia trachomatis infection was verified for 9 of 10 patients whose LCR specimens were positive but whose cultures were negative. Vaginal and cervical swab specimens were positive by LCR for 46 (93.9%) and 44 (89.8%) of 49 chlamydia-infected patients, respectively. These data suggest that LCR testing for chlamydia with vaginal swab specimens obtained by patients themselves is as sensitive as cervical LCR and more sensitive than cell culture.