Abstract: Background The organizational model of out-of-hours primary care is likely to affect healthcare use. We aimed to examine differences in the use of general practitioner cooperatives for out-of-hours care in the Netherlands and Belgium (Flanders) and explore if these are related to organizational differences. Methods A cross-sectional observational study using routine electronic health record data of the year 2016 from 77 general practitioner cooperatives in the Netherlands and 5 general practitioner cooperatives in Belgium (Flanders). Patient age, gender and health problem were analyzed using descriptive statistics. Results The number of consultations per 1000 residents was 2.3 times higher in the Netherlands than in Belgium. Excluding telephone consultations, which are not possible in Belgium, the number of consultations was 1.4 times higher. In Belgium, the top 10 of health problems was mainly related to infections, while in the Netherlands there were a larger variety of health problems. In addition, the health problem codes in the Dutch top 10 were more often symptoms, while the codes in the Belgian top 10 were more often diagnoses. In both countries, a relatively large percentage of GPC patients were young children and female patients. Conclusion Differences in the use of general practitioner cooperatives seem to be related to the gatekeeping role of general practitioners in the Netherlands and to organizational differences such as telephone triage, medical advice by telephone, financial thresholds and number of years of experience with the system. The information can benefit policy decisions about the organization of out-of-hours primary care.