A longstanding debate on health system organization relates to the benefits of integrating programs that emphasize specific interventions into mainstream health systems to increase access and improve health outcomes. This debate has long been characterized by polarization of views and ideologies, with protagonists for and against integration arguing relative merits of each approach. Recently, the debate has been rekindled due to substantial rises in externally funded programs for priority health, nutrition, and population (HNP) interventions and an increase in international efforts aimed at health system strengthening. In this paper the author present a conceptual framework and an analytical approach to define and assess the nature and extent of integration in relation to critical health system functions. The framework can also be used to systematically compare and contrast programs in different settings to generate meaningful evidence to inform policy. In this framework, the author defines integration as the extent, pattern, and rate of adoption and eventual assimilation of priority health interventions into each of the critical functions of a health system, which include, inter alia: (i) governance, (ii) financing, (iii) planning, (iv) service delivery, (v) monitoring and evaluation, and (vi) demand generation. The framework and the analytical approach are intended for evaluative and formative studies of policies, systems, and programs.