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Objective: To describe the implementation of a system-wide, electronic medical record (EMR)-based quality improvement intervention targeting medication reconciliation (MedRec) in outpatient pediatrics and to test variables associated with the performance of MedRec., Methods: This was a retrospective study using serial cross-sections of outpatient pediatric visits over a 5-year period set in a multispecialty children's integrated health care network in Florida, Delaware, Pennsylvania, and New Jersey. We reviewed 2 745 523 outpatient pediatric visits between 2005 and 2010. In 2007, the performance of MedRec was identified as critical to improving patient safety at our organization. A comprehensive intervention involved changes in the EMR, automated generation of medication lists, educational modules, and provider compliance reports. In 2009, quality-based financial incentives to physicians to perform MedRec were added. The outcome measure was documentation of MedRec performance., Results: MedRec improved consistently over time, from a nadir of 0% in 2005 to a maximum of 71% in 2010. Performance of MedRec varied according to practice location as the intervention was rolled out. Throughout the study period, documentation of MedRec was consistently less likely for sick visits (adjusted odds ratio [aOR] for each year ranged from 0.44 to 0.68) but more likely if the provider placed a medication order during the visit (aOR: 1.70-2.15). Beginning in 2009, visits with providers eligible for the quality-based financial incentive were more likely to have had MedRec performed (aOR: 2.02 [2009] and 2.31 [2010])., Conclusions: A system-wide, EMR-based, outpatient pediatric quality improvement intervention was successful in improving documentation of the performance of MedRec, a national patient safety goal.