OBJECTIVES: Treatment guidelines are an important source for estimation of resource use in pharmacoeconomic models. Observance of recommendation in clinical practice is a possible element of uncertainty in the assessment of the results. For prevention of stroke in patients with nonvalvular atrial fibrillation (AFib) a number of national and international guidelines exists. Up to now there was a lack of studies which analysed the use of guidelines in prevention of stroke in Germany. METHODS: A telephone interview was conducted with a cross-section of GPs, internists and cardiologists randomly selected from a sub-set of 7,072 out of the 59,953 office-based physicians of these specialities in Germany. A total of 75 completed surveys (15.1% of 498 eligible respondents) were completed. Beside questions on knowledge of the treatment guidelines the physicians were requested to assess three case vignettes with need of primary and secondary prevention strategies. RESULTS: A total of 22% of the physicians stated that they didn't know the national recommendations for stroke prevention. Especially GPs were uninformed. Only 66% of the GPs shared the opinion that guidelines are helpful for their daily clinical practice. On the basis of presented fictive patients the physicians showed a high degree of uncertainness. The unambiguous case were better rated by GPs, whereas more cardiologist and internists proposed treatments according to the guidelines in the more complex patients. In the primary prevention of stroke half of the respondents assed treatment with ASS in contrast with the guidelines as sensibly. In general physicians with higher qualification had better knowledge, but deficits exists independently from specialty. CONCLUSION: Results show heterogeneous use of treatment guidelines by German office-based physicians. In Germany, treatment guidelines don't reproduce the clinical practice and should be used as a reference in pharmacoeconomic studies with caution.