There is renewed concern over the sustainability of disease control programmes, and re-emergence of policy recommendations to integrate programmes with general health systems. However, the conceptualization of this issue has remarkably received little critical attention. Additionally, the study of programmatic sustainability presents methodological challenges. In this article, we propose a conceptual framework to support analyses of sustainability of communicable disease programmes. Through this work, we also aim to clarify a link between notions of integration and sustainability. As a part of development of the conceptual framework, we conducted a systematic literature review of peer-reviewed literature on concepts, definitions, analytical approaches and empirical studies on sustainability in health systems. Identified conceptual proposals for analysis of sustainability in health systems lack an explicit conceptualization of what a health system is. Drawing upon theoretical concepts originating in sustainability sciences and our review here, we conceptualize a communicable disease programme as a component of a health system which is viewed as a complex adaptive system. We propose five programmatic characteristics that may explain a potential for sustainability: leadership, capacity, interactions (notions of integration), flexibility/adaptability and performance. Though integration of elements of a programme with other system components is important, its role in sustainability is context specific and difficult to predict. The proposed framework might serve as a basis for further empirical evaluations in understanding complex interplay between programmes and broader health systems in the development of sustainable responses to communicable diseases.