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In the context of sector-wide approaches and the considerable funding being put into the health sectors of low-income countries, the need to invest in well-functioning national health sector monitoring and evaluation (M&E) systems is widely acknowledged. Regardless of the approach adopted, an important first step in any strategy for capacity development is to diagnose the quality of existing systems or arrangements, taking into account both the supply and demand sides of M&E. As no standardized M&E diagnostic instrument currently exists, we first invested in the development of an assessment tool for sector M&E systems. To counter the criticism that M&E is often narrowed down to a focus on technicalities, our diagnostic tool assesses the quality of M&E systems according to six dimensions: (i) policy; (ii) quality of indicators and data (collection) and methodology; (iii) organization (further divided into iiia: structure and iiib: linkages); (iv) capacity; (v) participation of non-government actors and (vi) M&E outputs: quality and use. We subsequently applied the assessment tool to the health sector M&E systems of Rwanda and Uganda, and this article provides a comparative overview of the main research findings. Our research may have important implications for policy, as both countries receive health sector (budget) support in relation to which M&E system diagnosis and improvement are expected to be high on the agenda. The findings of our assessments indicate that, thus far, the health sector M&E systems in Rwanda and Uganda can at best be diagnosed as ‘fragmentary’, with some stronger and weaker elements.