OBJECTIVE: To systematically review the literature on if and how HIV/AIDS and TB programmes have impacted on general healthcare systems in Association of Southeast Asian Nations (ASEAN) countries. METHODS: Medline, Embase, Global Health and CINHAL were searched for English language literature published between 1st January 2003 and 31st March 2011. Papers included had to focus on: HIV and/or TB control programmes; the low- and-middle-income ASEAN countries; and factors related to any health systems functions. The effects were examined along six system functions: Stewardship and Governance; Financing; Planning; Service Delivery; Monitoring and Evaluation; and Demand Generation. A comprehensive thematic analytical tool aligned with the above six health systems functions was developed to support data extraction and analysis. FINDINGS: 88 papers met the inclusion criteria. Most programme effects highlighted were related with health service delivery. The other five health system functions were seldom scrutinized, and each covered by less than a quarter of papers. Overall 69% of effects highlighted were positive effects whereas 31% were negative. CONCLUSION: There was a paucity of robust evidence. Effects on health systems were rarely a focus of research protocols but more often a minor component in the Results/Discussion sections. Particular attention should be paid by Global Health Initiatives to the negative effects that emerged from this study, such as the development of parallel systems, specific incentives not available to the general health systems, and lack of integration of services with private healthcare providers.