BACKGROUND: Chlamydia causes infertility and increases risk of HIV infection, and population-based studies provide essential information for effective infection control and prevention. This study examined Chlamydia trachomatis prevalence and risk factors among a representative sample of 18-49-year-old residents in Hong Kong. METHODS: Census boundary map of 412 constituency areas was used as primary sampling units to construct the sampling frame and, residential buildings and units were randomly selected using geospatial modelling. A questionnaire on sexual practice and health was conducted, and polymerase chain reaction was used to test the urine for genital chlamydial infection. Invitation letters were sent to the selected households and a team of interviewers were sent to recruit one subject per household. Prevalence data was weighted according to the 2011 census and risk factors identified through logistic regression. RESULTS: Among 881 participants (response rate of 24.5%), the overall Chlamydia trachomatis prevalence was low at 1.4% (95%CI 0.8-2.5%) but sexually active young (18-26 years) women had relatively high prevalence (5.8%, 95%CI 1.7-18.2%) in Hong Kong. A unique U-shape disease burden was observed with peaks in younger and older (40-49 years) women. Amongst the sexually active women, the risk factors of Chlamydia trachomatis infection were: younger age (aOR = 25.4, 95% CI 2.81-230); living alone (aOR = 8.99, 95% CI 1.46-55.40); and, among all the sexually active participants, males (including the male partners of the female participants) who had travelled out of Hong Kong in the previous 12 months had higher risks of infection (aOR = 5.35; 95% CI 1.25-22.8). A core-peripheral geographical distribution of Chlamydia trachomatis prevalence was also observed. CONCLUSION: Young and older sexually active women in Hong Kong have high prevalence of chlamydia. Routine screening for sexually active women and young men should be considered. Further research on testing feasibility and linkage-to-care are urgently needed to control the infection.