In Israel, diffusion of clinical information systems is almost universal in ambulatory medical services. The drug prescription module embedded in a widely-used electronic patient record system has the capacity to intervene and notify physicians about available generic or therapeutic substitute drugs, when their first choice is outside the insurer's preferred drug list. The objective of this paper is to study how such intervention influences drug prescription habits of physicians and helps contain costs. To this end we monitored system use for 40 weeks, recording physicians’ willingness to change their choice to a substitute following system notification. Findings show higher physician compliance with generic substitutes than with therapeutic substitutes, based on a cognitive decision process upon notification, and increase in compliance over time, until stabilization. The resulting direct financial savings on expenditure for drugs, estimated to be 4.7% for chronic drugs, entail long-term savings.