A Good Clinical Practices (GCPs) course, based on the combination of theoretical modules with a practical training in real-life conditions, was held in 2010 in Burkina Faso. It was attended by 15 trainees from nine African, Asian, and Latin American countries. There were some discrepancies between the average good results at the end of the theoretical phase and the GCP application during the first days of the practical phase, underlying the difficulties of translating theoretical knowledge into good practices. Most of the findings were not unexpected and reflected the challenges commonly faced by clinical investigators in resource-poor contexts (i.e., the high workload at peripheral health facilities, the need to conciliate routine clinical activities with clinical research, and the risk of creating a double standard among patients attending the same health facility [free care for recruited patients versus user fees for non-recruited patients with the same medical condition]). Even if limited in number and time, these observations suggest that a theoretical training alone may not be sufficient to prepare trainees for the challenges of medical research in real-life settings. Conversely, when a practical phase immediately follows a theoretical one, trainees can immediately experience what the research methodology implicates in terms of work organization and relationship with recruited and non-recruited patients. This initial experience shows the complexity of translating GCP into practice and suggests the need to rethink the current conception of GCP training.