Objective: a) To document the presence and use of clinical department systems (CDS) in a university hospital that implemented a hospital-wide electronic health record (EHR) in 1999 and b) To compare clinical use of the CDS with that of the EHR. Method: Identification of CDSs in use by contacting leaders and senior physicians at clinical departments at the hospital. Identification of key properties of each CDS by interviewing users. Results: We identified a total of 60 CDSs, of which 53 fell in one of four categories; Journal or documentation system tailored to a department or medical specialty (19 systems), Software bundled with electronic medical equipment (control/ storage/ presentation) (14 systems), Logistics/ administration/ planning/ appointments (10 systems) and Database for medical research (10 systems). Many CDSs were described to outperform the EHR system with regard to ability to provide better patient overview and better support for registering patient data. CDSs are not integrated with the EHR and thus contain islands of data. Conclusion: CDSs continue to fill important roles and there is no tendency towards that the hospital-wide EHR makes CDSs obsolete.