OBJECTIVE To investigate the possibility that infertile Nigerian women have a higher rate of cervical colonisation with pathogenic and facultative organisms than fertile controls. METHODS The prevalence of common microorganisms in the vagina and endocervical canals of infertile women was compared with that of pregnant controls. METHODS The Obafemi Awolowo University Hospital Maternity Centre. METHODS 92 infertile women were compared with 86 pregnant controls. METHODS rates of isolation of Neisseria gonorrhoeae, Candida albicans, Trichomonas vaginalis and other facultative organisms in cases and controls. RESULTS The rate of isolation of Neisseria gonorrheae was 17.4% among infertile women compared with 10.5% in the group of pregnant women (p > 0.05). There was no significant difference between the groups in the rate of isolation of Candida albicans, Trichomonas vaginalis and other facultative organisms. High rates of isolation of microorganisms were observed in both groups. However, women with secondary infertility had higher rate of carriage of Neisseria gonorrheae, Candida albicans and Staphylococcus aureus as compared with women with primary infertility. Nearly 15% of infertile women had previous episodes of pelvic inflammatory disease and 26% had had induced abortions. A positive history of vaginal discharge was a poor predictor of vagina and endocervical carriage of microorganisms. CONCLUSIONS High rates of pathogenic organisms exist in the lower genital tract of infertile women and controls. Women with secondary infertility are more likely to have pathogenic organisms than women with primary infertility. A policy of routinely screening women for lower genital tract infections should be pursued in this population because of the high rate of infection.