Several frameworks exist to analyse factors which influence the uptake of evidence into policy processes in resource poor settings, yet empirical analyses of health policy making in these settings are relatively rare. National policy making for cotrimoxazole preventive therapy in developing countries offers a pertinent case to apply a policy analysis lens. Comparative analysis was conducted in Malawi, Uganda and Zambia. We applied the ‘RAPID’ framework, and conducted in-depth interviews across the three countries to examine the influence of context, evidence, and links between researchers, policy makers and those seeking to influence policy processes. Each area of analysis was found to have an influence on the creation of national policy on cotrimoxazole preventive therapy (CPT) in all three countries. This analysis underscores the importance of considering national level variables in the explanation of the uptake of evidence into national policy settings, and recognising how local policy makers interpret international evidence.