Home testing for chlamydia and gonorrhea increases screening rates, but the cost consequences of this intervention are unclear. We examined the cost differences between home-based and clinic-based testing and the cost-effectiveness of home testing based on the DAISY study, a randomized controlled trial. Direct and indirect costs were estimated for home and clinic testing, and cost-effectiveness was calculated as cost per additional test performed. In the clinic testing group, direct costs were 49/test and indirect costs (the costs of seeking or receiving care) were 62/test. Home testing cost was 25/test. We found that home testing was cost saving when all testing for all patients was considered. However cost savings were not seen when only asymptomatic tests or when patient subgroups were considered. A home testing program could be cost saving, depending on whether changes in clinic testing frequency occur when home testing is available.