The Electronic Health Records for Clinical Research (EHR4CR) project aims to develop services and technology for the leverage reuse of Electronic Health Records with the purpose of improving the efficiency of clinical research processes. A pilot program was implemented to generate evidence of the value of using the EHR4CR platform. The user acceptance of the platform is a key success factor in driving the adoption of the EHR4CR platform; thus, it was decided to evaluate the user satisfaction. In this paper, we present the results of a user satisfaction evaluation for the EHR4CR multisite patient count cohort system. This study examined the ability of testers (n = 22 and n = 16 from 5 countries) to perform three main tasks (around 20 minutes per task), after a 30-minute period of self-training. The System Usability Scale score obtained was 55.83 (SD: 15.37), indicating a moderate user satisfaction. The responses to an additional satisfaction questionnaire were positive about the design of the interface and the required procedure to design a query. Nevertheless, the most complex of the three tasks proposed in this test was rated as difficult, indicating a need to improve the system regarding complicated queries.