Physicians' acceptance of Electronic Medical Record Systems (EMRs) is closely related to their usability. Knowledge about end-users' opinions on usability of an EMR system may contribute to planning for the next phase of the usability cycle of the system. A demand for integration of new functionalities, such as computerized order entry and an electronic patient status led to redesign of our EMR system, which had been in use for over 8 years at the Academic Medical Center of Amsterdam. The aim of this study was to understand whether the redesigned EMR system was an improvement of the earlier EMR and which system aspects accounted for user satisfaction and which did not. We conducted a formative pre- and post usability evaluation of our former and redesigned EMR system. For the assessment of both system versions' usability, we distributed two standardized usability questionnaires among 150 clinicians who routinely had used the older EMR system and had been working with its newer version for 6 weeks. Though overall user satisfaction was relatively high for both EMR systems, screen layout and interaction structure proved less easy to work with in the newer EMR system. The new EMR system however was more appreciated because of its enhanced functionality, capabilities and likeable user-interface. The results point to a number of actions that might be useful in future usability improvement efforts of our EMR system and other EMRs.