BACKGROUND: Providing HIV testing at health facilities remains the most common approach to ensuring access to HIV treatment and prevention services for the millions of undiagnosed HIV-infected individuals in sub-Saharan Africa. We sought to explore the costs of providing these services across three southern African countries with high HIV burden. METHODS: Primary costing studies were undertaken in 54 health facilities providing HIV testing services (HTS) in Malawi, Zambia and Zimbabwe. Routinely collected monitoring and evaluation data for the health facilities were extracted to estimate the costs per individual tested and costs per HIV-positive individual identified. Costs are presented in 2016 US dollars. Sensitivity analysis explored key drivers of costs. RESULTS: Health facilities were testing on average 2290 individuals annually, albeit with wide variations. The mean cost per individual tested was US$5.03.9 in Malawi, US$4.24 in Zambia and US$8.79 in Zimbabwe. The mean cost per HIV-positive individual identified was US$79.58, US$73.63 and US$178.92 in Malawi, Zambia and Zimbabwe respectively. Both cost estimates were sensitive to scale of testing, facility staffing levels and the costs of HIV test kits. CONCLUSIONS: Health facility based HIV testing remains an essential service to meet HIV universal access goals. The low costs and potential for economies of scale suggests an opportunity for further scale-up. However low uptake in many settings suggests that demand creation or alternative testing models may be needed to achieve economies of scale and reach populations less willing to attend facility based services.