Over the past few years concerns have been rising about the use of Evidence-Based Practice (EBP). We explored obstacles among Belgian physiotherapists to the implementation of EBP in clinical work. We used a qualitative research strategy based on five focus groups, organised between October 2004 and May 2005. Purposeful sampling was used to recruit 43 participants from diverse geographical regions in Flanders, working in different settings and with a variety of interest and expertise in EBP. Data collection and analysis were concurrent and guided by "grounded theory approach." A problem tree was developed. Important obstacles to the implementation of EBP include physiotherapists' lack of autonomy and authority to decide on patients' treatments or to negotiate with government. In addition, the lack of evidence, inaccessibility and inapplicability of scientific evidence, the economic parameters influencing government and physicians, the expectations from patients and a lack of motivation hamper the implementation of EBP. The problem tree developed reveals direct links between the lack of autonomy from physiotherapists and the dominant position from physicians in the Belgian health care system, which further impacts the boundaries between both professions and the weight of physiotherapists in governmental advisory boards. Direct access to physiotherapy has not yet been considered in Belgium. However, it could have major advantages for physiotherapists who are in favour of a more autonomous, professional status.