The objective of this paper is to present crucial factors for the acceptance among registered doctors and pharmacists of the Austrian ‘e-Medikation’ system which is aimed at providing, on a national level, complete and recent information on all the medication that was prescribed or dispensed to a patient. As the accompanying formative evaluation study of the pilot project showed different overall acceptance rates among participating physicians and pharmacists, a decision tree analysis of 30 standardized survey items was performed to identify crucial acceptance factors. For the physicians' group, only two items (fear of improper data use and satisfaction with software support) were crucial for overall e-Medikation acceptance. The analysis of the pharmacists' data resulted in five crucial factors primarily concerning functional aspects and the perceived benefits of e-Medikation. The results indicate that the acceptance among physicians and pharmacists depends on quite different factors. This must be taken into account during the planned rollout of e-Medikation or of comparable projects.