Electronic decision-support tools may help to improve management of hyperlipidemia and other chronic diseases. This study examined the impact of lipid management tools integrated into an electronic medical record (EMR) in primary care practices. This randomized controlled trial was conducted in a national network of physicians who use an outpatient EMR. Adult primary care physicians were randomized by office to receive an electronic form that was embedded in the EMR. The form contained prompts regarding suboptimal care based on Adult Treatment Panel-III (ATP-III) guidelines, as well as reporting tools to identify patients outside of office visits whose lipid management was suboptimal. All active patients, ages 20-79 years, whose physicians participated in the study, were categorized as high, moderate, or low cardiovascular risk, and the proportion who were tested for hyperlipidemia, at lipid goal, and on lipid-lowering medications if not at goal were measured according to ATP-III guidelines. A total of 105 physicians from 25 offices and 64,150 patients were included in the study. Outcomes improved for most measures from before to 1 year after the intervention (November 1, 2005 to October 31, 2006). However, after controlling for confounding variables and for clustering in multilevel modeling, only up-to-date lipid testing for high-risk patients was statistically better in the intervention group as compared to the control group (adjusted odds ratio 15.0, P < 0.05). This study showed few differences in quality of lipid management after implementing an EMR-based disease management intervention in primary care settings. Future studies may need to examine more comprehensive interventions that include office staff in a team approach to care.