Clinical Trial Recruitment Support Systems can booster patient inclusion of clinical trials by automatically analyzing eligibility criteria based on electronic health records. However, missing interoperability has hindered introduction of those systems on a broader scale. Therefore, our aim was to develop a recruitment support system based on FHIR R4 and evaluate its usage and features in a cardiology department. Clinical conditions, anamnesis, examinations, allergies, medication, laboratory data and echocardiography results were imported as FHIR resources. Clinical trial information, eligibility criteria and recruitment status were recorded using the appropriate FHIR resources without extensions. Eligibility criteria linked by the logical operation “OR” were represented by using multiple FHIR Group resources for enrollment. The system was able to identify 52 of 55 patients included in four clinical trials. In conclusion, use of FHIR for defining eligibility criteria of clinical trials may facilitate interoperability and allow automatic screening for eligible patients at multiple sites of different healthcare providers in the future. Upcoming changes in FHIR should allow easier description of “OR”-linked eligibility criteria.