Background Mortality rates from ischaemic heart disease have consistently been higher in East compared to West Germany both prior to and since reunification. Coronary care is inversely related to mortality from ischaemic heart disease. The objective of the present study was, therefore, to compare cardiovascular medication in East and West German patients following cardiac rehabilitation. Methods East German ( n=530) and West German ( n=1638) patients were included at admission to one of 18 rehabilitation centres. Inclusion criteria were myocardial infarction, coronary artery bypass grafting and percutaneous transluminal coronary angioplasty. The follow-up period was 12 months. Results At admission, East and West German patients differed with regard to sociodemographic variables, risk factors and medical conditions. At 12 months, a higher percentage of West compared to East German patients were prescribed β-blockers (71% vs. 65%, P=0.04) and lipid-lowering agents (64% vs. 55%, P=0.002). Angiotensin converting enzyme (ACE) inhibitors, on the other hand, were prescribed more frequently in the East compared to the West (60% vs. 48%, P<0.001). In multivariable analyses, region of residence remained a significant predictor for the prescription of lipid-lowering agents (East vs. West: OR 0.61, 95% CI 0.46–0.81) and ACE inhibitors (East vs. West: OR 1.78, 95% CI 1.33–2.39). Conclusion There is a considerable variation in the prescription of cardiovascular medication in secondary prevention within Germany. Some, but not all, of this variation can be explained by differences in patient characteristics.