This article presents a study to evaluate the accuracy of drug interaction (DI) alerts triggered by two electronic medical record (EMR) systems in primary healthcare. A scenario-based software architecture analysis methodology (SAAM) was used with drug-drug interaction (DDI) pairs in hypothetical patient scenarios. A literature search identified common drugs used in the management of conditions in the elderly population. Three reference programs determined the level of severity of drug interactions, and a common severity rating scale was adapted. The EMR systems showed a limited potential to identify 'severe' clinically significant DDIs and considerable probability for triggering spurious alerts. This may explain the overriding of DI alerts and the interruption of the workflow of users of EMR systems. Reasons for EMR system deficiency included unavailable updates or programming, database functioning discrepancies, and controversies in the clinical evidence.