SETTING: The National Tuberculosis Programmes in Egypt and Syria. OBJECTIVES: To calculate the costs and effectiveness of alternative ways of implementing TB control in Egypt and Syria, in order to illustrate the factors influencing the cost-effectiveness of TB treatment in middle-income countries. DESIGN: We compared the costs and cure rates in Egypt and Syria of the World Health Organization recommended directly observed treatment, short-course (DOTS) strategy and alternative strategies. The study included costs both to the health services and to the patient. RESULTS: In Egypt and Syria, the cost-effectiveness of DOTS implemented through the primary health care (PHC) system was respectively $258 and $243 per patient cured. This compares to a cost per patient cured of $297 (Egypt) and $693 (Syria) for alternative strategies implemented through specialist clinics. In Egypt, when DOTS is implemented through specialist chest clinics it costs $585 per patient cured. Hospitalisation costs either $1490, $1621 or $1699 per patient cured, depending on treatment delivery in the continuation phase. CONCLUSION: This study demonstrates that the move towards DOTS integrated at the PHC level has substantially improved the effectiveness of TB treatment in Egypt and Syria, without substantially increasing costs. An analysis of the different costs and effectiveness of the variety of TB treatment strategies has enabled both National Tuberculosis Programmes to expand DOTS and implement it in a way that takes into account limited resources and local health systems.