The use of standards and Integrating the Healthcare Enterprise (IHE) is a crucial technique for supporting, monitoring and controlling the integration profiles in healthcare organization systems. The risk of “no-interoperability” increases when several standards are used. Lack of experience in developing countries, particularly in Algeria, increases this risk. This article aims to suggest and present a methodology for selecting standards and IHE integration profiles in field of E-health in order to build a base-frame of the Algerian E-Health system. In fact, this base-frame must comply with international standards and perfectly adapted to medical processes, thru respecting IHE integration profiles.