Medical decision analysis (MDA) has played an important role in assisting infectious disease physicians make decisions associated with varying levels of complexity. Clinicians are often uncomfortable with some aspects of MDA, particularly when utilities are used as outcome measures. However, as the present paper outlines, MDA may use other outcome variables, including costs and disease complications. In this context, this explicit, reproducible analytic framework is an important tool in the area of infectious diseases, and is frequently applied to many situations, including cost effectiveness analyses, studies involving assessment of risks versus benefits of preventive and treatment strategies, and other situations. The objective of this paper is to assist infectious diseases clinicians to understand better the role of MDA in clinical practice. In this regard, the principles of MDA are reviewed and a common clinical example is used for illustrative purposes.