Aware of the potential benefits of health information technology (IT), many early adopting health systems have leveraged electronic health records (EHRs) for far more than point-of-care documentation. Many rely on these electronic data to conduct quality assurance, quality improvement (QI) and reporting; surveillance; operations research; and clinical and health services research. However, as these health systems have generated more electronic data—and from an increasingly diverse array of IT systems and sources—they have encountered challenges associated with accurately recording, reconciling, and contextualizing these data in a way that supports a multitude of potential uses. This report describes some of the key challenges to capturing and then extracting “research grade” data from health IT systems, and elaborates on the experiences of these six health system partners that, recognizing the value of using EHR data to support research, have devised approaches to mitigate these challenges.