OBJECTIVE: To measure the costs and estimate the cost-effectiveness of the ProTEST package of tuberculosis/human immunodeficiency virus (TB/HIV) interventions in primary health care facilities in Cape Town, South Africa. METHODS: We collected annual cost data retrospectively using ingredients-based costing in three primary care facilities and estimated the cost per HIV infection averted and the cost per TB case prevented. FINDINGS: The range of costs per person for the ProTEST interventions in the three facilities were: US$ 7-11 for voluntary counselling and testing (VCT), US$ 81-166 for detecting a TB case, US$ 92-183 for completing isoniazid preventive therapy (IPT) and US$ 20-44 for completing six months of cotrimoxazole preventive therapy. The estimated cost per HIV infection averted by VCT was US$ 67-112. The cost per TB case prevented by VCT (through preventing HIV) was US$ 129-215, by intensified case finding was US$ 323-664 and by IPT was US$ 486-962. Sensitivity analysis showed that the use of chest X-rays for IPT screening decreases the cost-effectiveness of IPT in preventing TB cases by 36%. IPT screening with or without tuberculin purified protein derivative screening was almost equally cost-effective. CONCLUSION: We conclude that the ProTEST package is cost saving. Despite moderate adherence, linking prevention and care interventions for TB and HIV resulted in the estimated costs of preventing TB being less than previous estimates of costs of treating it. VCT was less expensive than previously reported in Africa.