Background: Chlamydia trachomatis is one of the major causes of sexually transmitted infections throughout the world. It is the primary cause for pelvic inflammatory disease, tubal infertility and ectopic pregnancy in females. Most infections are asymptomatic and remain undetected. The burden of disease in the Kenyan population is not well characterised and few previous studies, done in Kenya, show the prevalence of genital Chlamydia infection in sexually active females. There is a need to define prevalence in our local population as a public health need and to determine whether rapid point-of-care testing should be incorporated as a component of sexually transmitted infection testing. Objective: To assess the public health burden of genital Chlamydia infection in sexually active women of reproductive age in an urban population within Nairobi. Methods: A cross-sectional study design was employed. All women attending the gynaecology and antenatal clinics at the two study sites were invited to consent to completion of a questionnaire and vaginal swab collection. Women who tested positive for Chlamydia were offered treatment, together with their partner(s), and advised to come for a follow-up test. Results: A total of 300 women were tested. The prevalence of genital Chlamydia trachomatis was found to be 6% (95% CI 3.31% - 8.69%). The prevalence was higher in women who represented a higher socioeconomic level, but this difference was not significant (OR = 2.7). Use of vaginal swabs was established to be a more acceptable form of sample collection. Conclusion: The prevalence of genital Chlamydia is significant in our female population. There is a justifiable need to institute opportunistic screening programs to reduce the burden of this disease. Rapid point-of-care testing as a potential component of sexually transmitted infection testing can be utilised.