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Background: Almost 50% of the Nepali health budget is made up of international aid. International Non-Governmental Organizations working in the field of health are able to channel their funds directly to grass root level. During a 2010 conference, the Secretary of Population stated that the government has full knowledge and control over all funds and projects coming to Nepal. However, there are no documents to support this. The study aims to assess government and partner perceptions on whether Government of Nepal currently has full knowledge of contributions of international aid organizations and International Non-Governmental Organizations to health in Nepal and to assess if the government is able to control all foreign contributions to fit the objectives of Second Long Term Health Plan (1997-2017). Methods: A qualitative study was performed along with available literature review. Judgmental and snowball sampling led to 26 in depth interviews with key informants from the government, External Development Partners and International Non-Governmental Organizations. Results were triangulated based on source of data. Representatives of the Department of Health Services declined to be interviewed. Data collection was done until researchers felt data saturation had been reached with each group of key informants. Results: While Ministry of Health and Population leads the sector wide approach that aims to integrate all donor and International Non-Governmental Organization contributions to health and direct them to the government's priority areas, questions were raised around its capacity to do so. Similarly, informants questioned the extent to which Social Welfare Council was able to control all International Non-Governmental Organizations contributions. Political tumult, corruption in the government, lack of human resources in the government, lack of coordination between government bodies, convoluted bureaucracy, and unreliability of donor and International Non- Governmental Organization contributions were identified as the main reasons for difficulties in aid integration. Conclusions: Despite its commitment to coordinate and control development assistance to the health sector, and its leadership position of the Sector Wide Approach, complete knowledge and effective coordination of all international contributions remains a challenge and is hampered by issues within the government as well as among External Development Partners and International Non-Governmental Organizations. [ABSTRACT FROM AUTHOR]