The HIV/AIDS, tuberculosis and malaria pandemics pose substantial challenges globally and to health systems in the countries they affect. This demands an institutional approach that can integrate disease control programmes within health and social care systems. Whilst integration is intuitively appealing, evidence of its benefits remains uncertain and evaluation is beset by lack of a common understanding of what it involves. The aim of this paper is to better define integration in health systems relevant to communicable disease control. We conducted a critical review of published literature on concepts, definitions, and analytical and methodological approaches to integration as applied to health system responses to communicable disease. We found that integration is understood and pursued in many ways in different health systems. We identified a variety of typologies that relate to three fundamental questions associated with integration: (1) why is integration a goal (that is, what are the driving forces for integration); (2) what structures and/or functions at different levels of health system are affected by integration (or the lack of); and (3) how does integration influence interactions between health system components or stakeholders. The frameworks identified were evaluated in terms of these questions, as well as the extent to which they took account of health system characteristics, the wider contextual environment in which health systems sit, and the roles of key stakeholders. We did not find any one framework that explicitly addressed all of these three questions and therefore propose an analytical framework to help address these questions, building upon existing frameworks and extending our conceptualization of the 'how' of integration to identify a continuum of interactions that extends from no interactions, to partial integration that includes linkage and coordination, and ultimately to integration. We hope that our framework may provide a basis for future evaluations of the integration of programmes and health systems in the development of sustainable and effective responses to communicable diseases.