We estimate costs and their predictors for three HIV prevention interventions in Kenya: HIV testing and counselling (HTC), prevention of mother-to-child transmission (PMTCT) and voluntary medical male circumcision (VMMC). As part of the ‘Optimizing the Response of Prevention: HIV Efficiency in Africa’ (ORPHEA) project, we collected retrospective data from government and non-governmental health facilities for 2011-12. We used multi-stage sampling to determine a sample of health facilities by type, ownership, size and interventions offered totalling 144 sites in 78 health facilities in 33 districts across Kenya. Data sources included key informants, registers and time-motion observation methods. Total costs of production were computed using both quantity and unit price of each input. Average cost was estimated by dividing total cost per intervention by number of clients accessing the intervention. Multivariate regression methods were used to analyse predictors of log-transformed average costs. Average costs were $7 and $79 per HTC and PMTCT client tested, respectively; and $66 per VMMC procedure. Results show evidence of economies of scale for PMTCT and VMMC: increasing the number of clients per year by 100% was associated with cost reductions of 50% for PMTCT, and 45% for VMMC. Task shifting was associated with reduced costs for both PMTCT (59%) and VMMC (54%). Costs in hospitals were higher for PMTCT (56%) in comparison to non-hospitals. Facilities that performed testing based on risk factors as opposed to universal screening had higher HTC average costs (79%). Lower VMMC costs were associated with availability of male reproductive health services (59%) and presence of community advisory board (52%). Aside from increasing production scale, HIV prevention costs may be contained by using task shifting, non-hospital sites, service integration and community supervision.