The increased sensitivities of nucleic acid amplification tests such as ligase chain reaction (LCR) have the potential to simplify specimen collection for gonorrhea diagnosis. In this study patients took their own vaginal swab specimens for gonorrhea culture and LCR testing. Immediately following specimen collection by patients, a trained clinician obtained endocervical swab specimens for the same tests. By using LCR to diagnose gonorrhea, 54 (17.5%) of 309 patients had positive tests. Forty-five patients with positive cervical LCR tests also had positive vaginal LCR tests; for one patient, only a cervical LCR specimen was positive, and for eight patients, only vaginal specimens were positive. For specimens from patients whose gonorrhea cultures were positive, all vaginal swab specimens were positive by LCR and 42 (91%) of 46 cervical swab specimens were positive by LCR. LCR-positive specimens from eight patients with negative cultures (four with positive vaginal specimens only, one with a positive cervical specimen only, and three with positive vaginal and cervical specimens) were further evaluated with unrelated probe sets for gonococcal pilin B. Following resolution of the discrepancies between culture-negative and LCR-positive specimens, a diagnosis of gonorrhea could be confirmed for 52 of 54 patients with positive LCR tests. LCR testing with vaginal swabs was 100% sensitive and 99.6% specific and had a positive predictive value of 98.1% and a negative predictive value of 100%. In this study LCR testing of vaginal swab specimens obtained by patients themselves was significantly more sensitive for gonorrhea diagnosis of women than cervical LCR or culture (100% versus 84.6% for cervical LCR or culture; Mantel-Haenszel chi-square test result, 8.58; P = 0.003).