Accurate clinical and laboratory data about sexually transmitted diseases (STD) prevalence in Guinea-Bissau are not available. These data are important, since HIV2 is prevalent in this country, rates of HIV1 are increasing and STDs facilitate HIV transmission. Since DNA amplification methods have demonstrated to accurately diagnose chlamydial infections and gonorrhoea, the Amplicor CT/NG PCR Assay with Internal Control of Amplification (Roche Diagnostic System, Branchburg, NJ, USA) was used to estimate the prevalence of Neisseria gonorrhoeae and Chlamydia trachomatis genital infections in STDs and Family Planning Clinic attenders in Bissau, from March to July 1997. Two hundred and two cervical swabs and 31 urethral swabs were examined. Two women were excluded from this study because their cervical swabs contained inhibitory substances. N. gonorrhoeae was identified in 34/200 (17%) women and in 12/31 (38.7%) men. C. trachomatis was detected in 8/200 (4%) women there were no positive C. trachomatis results among the 31 men with urethritis. One woman presented a mixed infection with both organisms. The prevalence difference between men and women was not statistically significant (P=0.6) for C. trachomatis infection, but it was significant for N. gonorrhoeae infection (P=0.01). The prevalence rates of these infections found in this study, support the need for an urgent strategy to control STD in the region.