Clinical decision making (CDM) describes a form of qualitative inquiry that examines the thought processes involved in making medical decisions. A significant body of literature exists on the orderly "hypothetico-deductive" model of clinical decision making. However, very little has been written on how CDM differs in the acute setting. This paper reviews the common methods of CDM and their relevance to emergency medicine (EM). The concept of diagnostic uncertainty and the utility of the diagnosis of unknown etiology in the disposition phase of the emergency patient visit are discussed. Finally, a unique EM perspective on clinical decision-making errors is presented.