While medications can improve patients' health, the process of prescribing them is complex and error prone, and medication errors cause many preventable injuries. Computer provider order entry (CPOE) with clinical decision support (CDS), can improve patient safety and lower medication-related costs. To realize the medication-related benefits of CDS within CPOE, one must overcome significant challenges. Healthcare organizations implementing CPOE must understand what classes of CDS their CPOE systems can support, assure that clinical knowledge underlying their CDS systems is reasonable, and appropriately represent electronic patient data. These issues often influence to what extent an institution will succeed with its CPOE implementation and achieve its desired goals. Medication-related decision support is probably best introduced into healthcare organizations in two stages, basic and advanced. Basic decision support includes drug-allergy checking, basic dosing guidance, formulary decision support, duplicate therapy checking, and drug-drug interaction checking. Advanced decision support includes dosing support for renal insufficiency and geriatric patients, guidance for medication-related laboratory testing, drug-pregnancy checking, and drug-disease contraindication checking. In this paper, the authors outline some of the challenges associated with both basic and advanced decision support and discuss how those challenges might be addressed. The authors conclude with summary recommendations for delivering effective medication-related clinical decision support addressed to healthcare organizations, application and knowledge base vendors, policy makers, and researchers.