Fuzzy Cognitive Maps (FCMs) are a soft computing technique that follows an approach similar to human reasoning and human decision-making process, considering them a valuable modeling and simulation methodology. FCMs can successfully represent knowledge and experience, introducing concepts for the essential elements and through the use of cause and effect relationships among the concepts Medical Decision Systems are complex systems consisting of irrelevant and relevant subsystems and elements, taking into consideration many factors that may be complementary, contradictory, and competitive; these factors influence each other and determine the overall diagnosis with a different degree. Thus, FCMs are suitable to model Medical Decision Support Systems and the appropriate FCM structures are developed as well as corresponding examples from two medical disciplines, i.e. speech and language pathology and obstetrics, are described.