OBJECTIVE: The aim of the current study is to identify the output of French university hospitals in the Web of Science database and to perform a comparative bibliometric analysis to characterize their position in the national biomedical research landscape. METHODS: The first stage consisted in creating the unified "Organization-Enhanced" records in the Web of Science for 32 university hospitals, in order to ensure the reliable aggregated data. The research output of university hospitals and organizations members of the French National Alliance for Life Sciences and Health (Aviesan) are analyzed using bibliometric indicators, including the number of publications, category normalized citation impact, top one percent and top 10 percent of the most cited papers, international collaboration rate. RESULTS: In terms of publication output, university hospitals rank 3rd in France, after universities and CNRS. They contribute to about 17 % of the total national production and to 2.5 % of the European publications (EU28). Over the 10 years period, the impact of the papers produced by university hospitals grows faster than volume. Visibility and impact comply with the university hospitals' core assignments: teaching, research and knowledge transfer. CONCLUSIONS: This study provides objective data showing a leading position of the university hospitals among the biomedical research organizations in France, playing a major role in patient-based research.