A longstanding debate on health systems organization relates to benefits of integrating health programmes 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 the relative merits of each approach. However, all too frequently these arguments have not been based on hard evidence. The presence of both integrated and non-integrated programmes in many countries suggests there may be benefits to either approach, but the relative merits of integration in various contexts and for different interventions have not been systematically analysed and documented. In this paper we present findings of a systematic review that explores a broad range of evidence on: (i) the extent and nature of the integration of targeted health programmes that emphasize specific interventions into critical health systems functions, (ii) how the integration or non-integration of health programmes into critical health systems functions in different contexts has influenced programme success, (iii) how contextual factors have affected the extent to which these programmes were integrated into critical health systems functions. Our analysis shows few instances where there is full integration of a health intervention or where an intervention is completely non-integrated. Instead, there exists a highly heterogeneous picture both for the nature and also for the extent of integration. Health systems combine both non-integrated and integrated interventions, but the balance of these interventions varies considerably.