The main question in this paper was to look at the distribution of auxotypes and serovars of Neisseria gonorrhoeae and check whether they correlate with clinical symptoms/signs among female sex workers (FSW) from Kinshasa, Zaïre. The subject were 1233 FSW enrolled in a cross sectional study on STDs and HIV infection in 1988; 771 of them were followed prospectively for a median duration of 23 months. At each visit, clinical symptoms and signs of cervicitis were recorded and the subjects were screened for gonococcal and chlamydial infection. The pre-dominant auxotypes were prototrophic (35.2%), proline requiring (29.6%), and proline requiring phenylalanine inhibition (19%). Serovars 1A-6 (42.5%) and 1B-1 (16.7%) were the commonest. Infection with auxotype prototrophic and phenylalanine inhibition (Proto/Phenali) was significantly associated with both mucopurulent cervicitis and pelvic inflammatory disease; (OR = 8.9; p = 0.002 and OR =19 x9; p = 0.002; respectively). Despite the few associations found in this study, there was not clear pattern linking clinical manifestations to auxotype/serovar profiles.