This case study on Vietnam aims to generate empirical evidence on the relative merits of integration of two priority health interventions, HIV/AIDS and tuberculosis (TB), into six functions of the wider health system: stewardship and governance, service delivery, demand generation, monitoring and evaluation, planning, and financing. Selective documentary reviews and 25 qualitative, semi-structured interviews were conducted in early 2009 in Hanoi, Hai Duong province, Chih Linh district and Hoang Tien commune with informants from international, national and sub-national agencies steering or managing the HIV/AIDS and TB programmes and from health facilities providing HIV/AIDS and TB services. Data collected were collated and evaluated against 25 elements of integration. Each element of integration was ultimately classified as being 'fully/predominantly integrated', 'partially integrated', 'not or predominantly not integrated'. The results showed that none of the six programme functions was fully integrated into the general health care system as a whole. They were established either in parallel, notably at higher administrative levels, or were partially integrated. The study findings also revealed that little integration across all functional levels has occurred between the two programmes. Generally international agencies and sub-national domestic stakeholders supported more integration between vertical programmes (HIV and TB) and the general health systems, while national bodies responsible for HIV and TB favoured reinforcing a more vertical and thus less integrated approach. In the absence of shared assumptions and goals, this polarization of views may result in sub-optimal effectiveness and efficiency of each of the disease programmes as well as of HIV/TB interventions.