Attempts to comparatively analyse large-scale communicable disease control programmes have, for the most part, neglected the wider health system contexts within which the programmes lie. In addition, many evaluations of the integration of vertical disease control programmes into health systems have focused on single case studies or on a limited number of cases, or, when large numbers of cases were drawn upon, have been presented as a compendium of monographs rather than a systematic cross-national comparison. One reason for this may be that appropriate theories and tools for comparative health systems analysis are rare and difficult to formulate. In this paper we propose a conceptual framework and an analytical methodology which might be used to comparatively analyse a series of case studies that explore health systems, communicable diseases programmes and concepts of integration in order to make systematic comparisons to offer novel insights, to test new theories and to offer new hypotheses. We illustrate through a preliminary analysis how this framework can be applied to compare the impact of health systems integration and HIV and TB programmes in four countries in South-East Asia that were the subject of cases studies.