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Objective/Background  The Global Fund to Fight AIDS, Tuberculosis & Malaria (GF) strives for high value for money, encouraging countries to integrate synergistic services and systems strengthening to maximize investments. The GF needs to show how, and how much, its grants support more than just HIV/AIDS, TB and malaria.  Sexual and Reproductive Health (SRH) has been part of HIV/AIDS grants since 2007. Previous studies showed the GF PBF system does not allow resource tracking for SRH integration within HIV/AIDS grants. We present findings from a resource tracking case study using primary data collected at country level.    Methods  Ethiopia was the study site. We reviewed data from four HIV/AIDS grants from January 2009-June 2011 and categorized SDAs and activities as directly, indirectly, or not related to SRH integration. Data included: GF PBF data; financial, performance, in-depth interview and facility observation data from Ethiopia.    Results  All HIV/AIDS grants in Ethiopia support SRH integration activities (12-100%). Using activities within SDAs, expenditures directly supporting SRH integration increased from 25% to 66% for the largest HIV/AIDS grant, and from 21% to 34% for the smaller PMTCT-focused grant. Using SDAs to categorize expenditures underestimated direct investments in SRH integration; activity-based categorization is more accurate.  The important finding is that primary data collection could not resolve the limitations in using GF GPR data for resource tracking. The remedy is to require existing activity-based budgets and expenditure reports as part of PBF reporting requirements, and make them available in the grant portfolio database. The GF should do this quickly, as it is a serious shortfall in the GF guiding principle of transparency.    Conclusions  Showing high value for money is important for maximizing impact and replenishments. The Global Fund should routinely track HIV/AIDs grant expenditures to disease control, service integration, and overall health systems strengthening. The current PBF system will not allow this. Real-time expenditure analysis could be achieved by integrating existing activity-based financial data into the routine PBF system. The GF’s New Funding Model and the 2012-2016 strategy present good opportunities for over-hauling the PBF system to improve transparency and allow the GF to monitor and maximize value for money.    Electronic supplementary material  The online version of this article (doi:10.1186/s12992-015-0106-z) contains supplementary material, which is available to authorized users.

Tracking Global Fund HIV/AIDS resources used for sexual and reproductive health service integration: case study from Ethiopia