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This study aimed to determine the role of electronic health record software in resident education by evaluating documentation of 30 elements extracted from the American Academy of Ophthalmology Dry Eye Syndrome Preferred Practice Pattern. The Kresge Eye Institute transitioned to using electronic health record software in June 2013. We evaluated the charts of 331 patients examined in the resident ophthalmology clinic between September 1, 2011, and March 31, 2014, for an initial evaluation for dry eye syndrome. We compared documentation rates for the 30 evidence-based elements between electronic health record chart note templates among the ophthalmology residents. Overall, significant changes in documentation occurred when transitioning to a new version of the electronic health record software with average compliance ranging from 67.4% to 73.6% (p < 0.0005). Electronic Health Record A had high compliance (>90%) in 13 elements while Electronic Health Record B had high compliance (>90%) in 11 elements. The presence of dialog boxes was responsible for significant changes in documentation of adnexa, puncta, proptosis, skin examination, contact lens wear, and smoking exposure. Significant differences in documentation were correlated with electronic health record template design rather than individual resident or residents' year in training. Our results show that electronic health record template design influences documentation across all resident years. Decreased documentation likely results from "mouse click fatigue" as residents had to access multiple dialog boxes to complete documentation. These findings highlight the importance of EHR template design to improve resident documentation and integration of evidence-based medicine into their clinical notes.