Background The oral anticoagulant therapy - provided to prevent thrombosis - is known to be associated with substantial avoidable hospitalization. Improving the quality of the oral anticoagulant therapy could avoid drug related hospitalizations. Therefore, this study compared the patient outcomes between Dutch anticoagulant clinic (AC) regions taking the variation in chronic care management into account in order to explore whether chronic care management elements could improve the quality of oral anticoagulant therapy. Methods Two data sources were combined. The first source was a questionnaire that was send to all ACs in the Netherlands in 2008 (response = 100%) to identify the application of chronic care management elements in the AC regions. The Chronic Care Model of Wagner was used to make the concept of chronic care management operational. The second source was the report of the Dutch National Network of ACs which contains patient outcomes of the ACs. Results Patient outcomes achieved by the ACs were good, yet differences existed; for instance the percentage of patients in the appropriate therapeutic ranges varied from 67 to 87% between AC regions. Moreover, differences existed in the use of chronic care management elements of the chronic care model, for example 12% of the ACs had multidisciplinary meetings and 58% of the ACs had formal agreements with at least one hospital within their region. Patient outcomes were significantly associated with patient orientation and the number of specialized nurses versus doctors (p-values < 0.05). Furthermore, the overall extent to which chronic care management elements were applied was positively associated with patient outcomes (p-values < 0.05). Conclusions Substantial differences in the patient outcomes as well as chronic care management of oral anticoagulant therapy existed. Since our results showed a positive association between overall application of chronic care management and patient outcomes, additional research is needed to fully understand the working mechanism of chronic care management.