Health systems in central Asia (the former Soviet Union) face challenges to control TB and HIV/AIDS epidemics. Integration of communicable disease control programmes with the broader health system has been recommended to ensure programmes' sustainability. An important constraint for studying sustainability and integration has been a lack of conceptual clarity. Drawing on a critical assessmenot f publishedl iterature, a novel conceptualf ramework for the analysis of sustainability and integration in health systems has been developed. A sustainablec ommunicabled iseasep rogrammei s defined as continuouslye ffective in reducinga disease problem, responsive and adaptive to changes in the nature of disease epidemics, population needs or the contextual environment. Sustainability of a programme is conceptualised as having five dimensions: leadership, capacity, interactions, flexibility (adaptability) and performance (effectiveness, efficiency, equity). Existing frameworks of integration and health systems have been extended; defining levels of formal interactions between the system components. The research applied a case study approach. The case study was conducted in Kyrgyzstan, and relied on documentary review, qualitative interviews with key informants, and framework analysis. This study revealed several inter-related factors that affect the potential for sustainability of TB and HIV/AIDS programmes in Kyrgyzstan. Among overarching challenges for sustainability of both programmes are overall weak capacity of the health system and the reliance on international assistance for implementing the efforts to control the epidemics. This thesis highlights the importance of health system's structural and functional arrangements in sustaining the programmes into the future. In Kyrgyzstan, the factors such as fragmentation of governance and financing impede the development of effective interactions at the level of service delivery. In turn, fragmentation of service delivery remains the key impediment for efficiency, effectiveness and equity of disease control interventions. The prospects for sustainability of both programmes are constrained by institutional interests of domestic and international actors, who rarely consider the central question for sustainability that is efficiency of resources allocation and use. Weak disease surveillance and M&E systems emerged as one of the key barrier for development of effective disease control policies in the country and efficient planning of resources. Because of weaknesses of surveillance, this study could not provide the answer whether disease control efforts have resulted in the reduction of mortality and morbidity associated with TB and/or HIV/AIDS.