OBJECTIVE: To develop a methodology and an instrument that allow the simultaneous rapid and systematic examination of the broad public health context, the health care systems, and the features of disease-specific programmes. METHODS: Drawing on methodologies used for rapid situational assessments of vertical programmes for tackling communicable disease, we analysed programmes for the control human of immunodeficiency virus (HIV) and their health systems context in three regions in the Russian Federation. The analysis was conducted in three phases: first, analysis of published literature, documents and routine data from the regions; second, interviews with key informants, and third, further data collection and analysis. Synthesis of findings through exploration of emergent themes, with iteration, resulted in the identification of the key systems issues that influenced programme delivery. FINDINGS: We observed a complex political economy within which efforts to control HIV sit, an intricate legal environment, and a high degree of decentralization of financing and operational responsibility. Although each region displays some commonalities arising from the Soviet traditions of public health control, there are considerable variations in the epidemiological trajectories, cultural responses, the political environment, financing, organization and service delivery, and the extent of multisectoral work in response to HIV epidemics. CONCLUSION: Within a centralized, post-Soviet health system, centrally directed measures to enhance HIV control may have varying degrees of impact at the regional level. Although the central tenets of effective vertical HIV programmes may be present, local imperatives substantially influence their interpretation, operationalization and effectiveness. Systematic analysis of the context within which vertical programmes are embedded is necessary to enhance understanding of how the relevant policies are prioritized and translated to action.