OBJECTIVE: We explored how patients from Sub Saharan Africa (SSA) infected with HIV and living in Switzerland, and their treating physicians perceived their health, whether these perceptions correlated with biological markers, and what organisational changes participants considered likely to improve quality of care. METHODS: A prospective standardized questionnaire was submitted to HIV-infected patients from SSA and their physicians. Results were correlated with biological data. RESULTS: While physicians deduced improved health status from laboratory results, these did not provide an adequate surrogate marker of good health for patients. Patients experienced important social and economical difficulties with adverse consequences on their mental health. They requested social assistance, whereas physicians sought improved cultural competency. CONCLUSION: Patients and physicians did not agree in their evaluation of patients' health status. Patients did not perceive their health through biological markers, but linked their mental health with their socioeconomic context. Physicians underestimated patients' biological health and their evaluation of global health. PRACTICE IMPLICATIONS: Exploring difficulties perceived by physicians with specific patients lead to identification of structural weaknesses, resulting in suggestions to improve physicians' medical training and patients' care. This illustrates the importance of accessing patients' perspective and not relying solely on physicians' perception of the problem.