The potential impacts of climate change on human health in sub-Saharan Africa are wide-ranging, complex, and largely adverse. The region’s Indigenous peoples are considered to be at heightened risk given their relatively poor health outcomes, marginal social status, and resource-based livelihoods; however, little attention has been given to these most vulnerable of the vulnerable. This paper contributes to addressing this gap by taking a bottom-up approach to assessing health vulnerabilities to climate change in two Batwa Pygmy communities in rural Uganda. Rapid Rural Appraisal and PhotoVoice field methods complemented by qualitative data analysis were used to identify key climate-sensitive, community-identified health outcomes, describe determinants of sensitivity at multiple scales, and characterize adaptive capacity of Batwa health systems. The findings stress the importance of human drivers of vulnerability and adaptive capacity and the need to address social determinants of health in order to reduce the potential disease burden of climate change