BACKGROUND: The prevalence of hypertension and diabetes are expected to increase in sub-Saharan Africa over the next decade. Some studies have documented that lifestyle factors and lack of awareness are directly influencing the control of these diseases. Yet, few studies have attempted to understand the barriers to control of these conditions in rural settings. The main objective of this study was to understand the challenges to hypertension and diabetes care in rural Uganda. METHODS: We conducted semi-structured interviews with 24 patients with hypertension and/or diabetes, 11 health care professionals (HCPs), and 12 community health workers (known as village health team members [VHTs]) in Nakaseke District, Uganda. Data were coded using NVivo software and analyzed using a thematic approach. RESULTS: The results replicated several findings from other settings, and identified some previously undocumented challenges including patients' knowledge gaps regarding the preventable aspects of HTN and DM, patients' mistrust in the Ugandan health care system rather than in individual HCPs, and skepticism from both HCPs and patients regarding a potential role for VHTs in HTN and DM management. CONCLUSIONS: In order to improve hypertension and diabetes management in this setting, we recommend taking actions to help patients to understand NCDs as preventable, for HCPs and patients to advocate together for health system reform regarding medication accessibility, and for promoting education, screening, and monitoring activities to be conducted on a community level in collaboration with village health team members.