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Abstract Background Faced with patients suffering from more than one chronic condition, or multimorbidity, general practitioners (GPs) must establish diagnostic and treatment priorities. Patients also set their own priorities to handle the everyday burdens associated with their multimorbidity and these may be different from the priorities established by their GP. A shared patient–GP agenda, driven by knowledge of each other’s priorities, would seem central to managing patients with multimorbidity. We evaluated GPs’ ability to identify the health condition most important to their patients. Methods Data on 888 patients were collected as part of a cross-sectional Swiss study on multimorbidity in family medicine. For the main analyses on patients-GP agreement, data from 572 of these patients could be included. GPs were asked to identify the two conditions which their patient considered most important, and we tested whether either of them agreed with the condition mentioned as most important by the patient. In the main analysis, we studied the agreement rate between GPs and patients by grouping items medically-related into 46 groups of conditions. Socio-demographic and clinical variables were fitted into univariate and multivariate models. Results In 54.9% of cases, GPs were able to identify the health condition most important to the patient. In the multivariate model, the only variable significantly associated with patient–GP agreement was the number of chronic conditions: the higher the number of conditions, the less likely the agreement. Conclusion GPs were able to correctly identify the health condition most important to their patients in half of the cases. It therefore seems important that GPs learn how to better adapt treatment targets and priorities by taking patients’ perspectives into account.