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Background: The Northwestern University Center for Education and Research on Therapeutics (CERT), funded by the Agency for Healthcare Research and Quality, is one of seven such centers in the USA. The thematic focus of the Northwestern CERT is 'Tools for Optimizing Medication Safety.' Ensuring drug safety is essential, as many adults struggle to take medications, with estimates indicating that only half of adults take drugs as prescribed. This report describes the methods and rationale for one innovative project within the CERT: the 'Primary Care, Electronic Health Record-Based Strategy to Promote Safe and Appropriate Drug Use'. Methods/Design: The overall objective of this 5-year study is to evaluate a health literacy-informed, electronic health record-based strategy for promoting safe and effective prescription medication use in a primary care setting. A total of 600 English and Spanish-speaking patients with diabetes will be consecutively recruited to participate in the study. Patients will be randomized to receive either usual care or the intervention; those in the intervention arm will receive a set of print materials designed to support medication use and prompt provider counseling and medication reconciliation. Participants will be interviewed in person after their index clinic visit and again one month later. Process outcomes related to intervention delivery will be recorded. A medical chart review will be performed at 6 months. Patient outcome measures include medication understanding, adherence and clinical measures (hemoglobin A1c, blood pressure, and cholesterol; exploratory outcomes only). Discussion: Through this study, we will be able to examine the impact of a health literacy-informed, electronic health record-based strategy on medication understanding and adherence among diabetic primary care patients. The measurement of process outcomes will help inform how the strategy might ultimately be refined and disseminated to other sites. Strategies such as these are needed to address the multifaceted challenges related to medication self-management among patients with chronic conditions. [ABSTRACT FROM AUTHOR]