BACKGROUND In many countries, financial assistance is awarded to physicians who settle in an area that is designated as a shortage area to prevent unequal accessibility to primary health care. Today, however, policy makers use fairly simple methods to define health care accessibility, with physician-to-population ratios (PPRs) within predefined administrative boundaries being overwhelmingly favoured. Our purpose is to verify whether these simple methods are accurate enough for adequately designating medical shortage areas and explore how these perform relative to more advanced GIS-based methods. METHODS Using a geographical information system (GIS), we conduct a nation-wide study of accessibility to primary care physicians in Belgium using four different methods: PPR, distance to closest physician, cumulative opportunity, and floating catchment area (FCA) methods. RESULTS The official method used by policy makers in Belgium (calculating PPR per physician zone) offers only a crude representation of health care accessibility, especially because large contiguous areas (physician zones) are considered. We found substantial differences in the number and spatial distribution of medical shortage areas when applying different methods. CONCLUSIONS The assessment of spatial health care accessibility and concomitant policy initiatives are affected by and dependent on the methodology used. The major disadvantage of PPR methods is its aggregated approach, masking subtle local variations. Some simple GIS methods overcome this issue, but have limitations in terms of conceptualisation of physician interaction and distance decay. Conceptually, the enhanced 2-step floating catchment area (E2SFCA) method, an advanced FCA method, was found to be most appropriate for supporting areal health care policies, since this method is able to calculate accessibility at a small scale (e.g., census tracts), takes interaction between physicians into account, and considers distance decay. While at present in health care research methodological differences and modifiable areal unit problems have remained largely overlooked, this manuscript shows that these aspects have a significant influence on the insights obtained. Hence, it is important for policy makers to ascertain to what extent their policy evaluations hold under different scales of analysis and when different methods are used.