Electronic health records (EHRs) have been shown to reduce medication errors, improve patient outcomes, and create administrative efficiencies. Numerous public and private efforts are currently underway to achieve universal EHR adoption in the United States by the year 2014. EHRs hold a great potential to integrate clinical care and research by allowing input of clinical data in a structured format, facilitating electronic data capture for clinical trials and providing linkage with genomic information. The goal of this article is to inform the academic gastrointestinal community about the research opportunities created by the widespread adoption of EHRs and present a systematic approach in utilizing EHR-derived data for observational, experimental, or translational studies.