Background: Target groups for seasonal influenza vaccination are defined at the country level and are based on several factors. However, little is known about the national decision-making procedures. Objective: The purpose of this study was to compare the evidence used for the development of recommendations and its impact on the choice of target groups in France and the Netherlands. Methods: A preliminary documentary analysis identified institutions to include in the assessment: governmental authorities, research institutions, associations, and manufacturers. At least one expert from each group was invited to our study. Thirty-three semi structured interviews were conducted in 2013 (16 France, 17 the Netherlands). We used NVivo108 to perform a thematic content analysis. Results: Clinical/epidemiological studies were the evidence most used in both countries. Economic models were increasingly being used; these had greater influence on the decision making in the Netherlands than in France, probably because of the presence of a modeler. Generally, the quality of the evidence used was poor, although no systematic use of standard protocol for its assessment was observed. A general protocol was sometimes used in France; however, the personal judgment of the experts was crucial for the assessment in both countries. Conclusions: There were differences in the target groups, for example, pregnant women, recommended only in France. France and the Netherlands use similar evidence for developing vaccination recommendations, although different decisions are sometimes made regarding target groups. This could be associated with the lack of systematic standard appraisals, increasing the influence of the experts' judgment on decision making. The development of standards for the appraisal of evidence is recommended.