OBJECTIVE: To assess the cost-effectiveness of pharmacotherapy for partners in a screening program for asymptomatic infection with Chlamydia trachomatis (CT) in women. METHODS: A decision-analysis model was constructed for the health outcomes of a CT screening program, such as averted cases of pelvic inflammatory disease and infertility (major outcomes). Prevalence estimates of CT-infection and information on partner referral were derived from pilot studies in Amsterdam (the Netherlands). Reinfection due to failed partner referral or non-compliance with partner pharmacotherapy was included in the model. Cost-effectiveness from a societal perspective was estimated for a screening program in General Practices in Amsterdam, directed at women aged 15-29. For diagnosis of asymptomatic CT infection a Ligase Chain Reaction test on urine was used, for pharmacotherapy of women and partners azithromycin was used. By linking health outcomes with health-care costs and productivity losses averted costs were estimated. Cost-effectiveness was expressed as net costs per major outcome averted and was calculated in the reference case and in sensitivity analysis. RESULTS: Partner pharmacotherapy induces reductions of approximately 50% in net costs per major outcome averted of the screening program. Within the broader framework of the screening program partner pharmacotherapy is a cost-saving activity. CONCLUSIONS: Inclusion of partner pharmacotherapy provides significant improvements in overall cost-effectiveness of the CT-screening program. Partner pharmacotherapy lowers net costs per major outcome averted to realms where implementation of the screening program for women aged 15-29 should be considered. Implementation of the program is currently discussed for the city of Amsterdam. Given the cost-saving potentials, male partner pharmacotherapy should be pursued within broader framework of a CT-screening program for women.