Objectives: Ordinary electronic health record (EHR) systems have difficulty managing paper-based medical records because digitized paper-based records must be browsed with a viewer other than the main display for the EHR system. Because of this "fragmentation" of electronic and paper information, it is difficult to combine keyboard/ mouse input with handwriting input in a clinical setting. We developed a new EHR system to address this problem. Methods: We revised a commercial EHR system to function as a progress note system that integrates keyboard/ mouse-based electronic records with digitized paper-based records, both of which can be viewed in a page-turning style. In this system all records, including paper-based records, are arranged in relation to the time they were written, even when they were digitized later at a scanning center. These features of the system allow for combined use of handwritten and keyboard/mouse input, without fragmentation. We investigated the impact of the introduction of the first EHR system in the ophthalmology department at our hospital, which had long resisted implementation of an EHR system. Results: The number of ophthalmology outpatients did not significantly decrease after introduction of the system. The ophthalmologists in our hospital accepted the first EHR system without negative reactions, and a gradual transition from handwritten input to keyboard/mouse input was noted. Conclusions: The present system enables users to produce flexible medical documentation, by using both keyboard/mouse and handwriting inputs, without reducing medical efficiency or safety. This is a cost-efficient, true hybrid digital-analog EHR system.