BackgroundSwiss national surveillance of influenza vaccination uptake rates (VURs) relies on self‐reported vaccination status. The aim of this study was to determine VURs among at‐risk patients, namely, patients ≥65 of age and adult patients with chronic diseases, using claims data, instead of self‐reported measures, to investigate factors of vaccine uptake, and to assess different methodological approaches to conduct vaccination surveillance.MethodsIn this retrospective cross‐sectional analysis, we determined VURs in three influenza seasons (2015/2016–2017/2018). Medication, diagnosis, or medical services claims were used as triggers to identify patients. For the calculation of VURs in patients with chronic diseases, we identified those by triggers in the given season only (Model 1) and in the given and previous seasons (Model 2). Regression analysis was used to identify factors associated with vaccination status.ResultsData from 214,668 individual patients were analyzed. VURs over all seasons ranged from 18.4% to 19.8%. Most patients with chronic diseases were identified with the medication trigger, and we found no clinical significant differences in VURs comparing both models. Having a chronic disease, age, male gender, and regular health care provider visits were associated with increased odds of being vaccinated.ConclusionsVURs were below the recommended thresholds, and our analysis highlighted the need for efforts to increase VURs. We assessed the identification of chronic diseases by medication claims and the calculation of VURs based on data of the given season only as an effective approach to conduct vaccination surveillance. Claims data‐based surveillance may complete the national surveillance.