Root-filled teeth presenting with signs of post-treatment disease is a common finding in virtually every dental practice. There is both empirical and experimental evidence that, as long as the condition is asymptomatic, it is often left untreated. Professional judgements and decision making in endodontics as in any medical discipline are based on qualified estimations of the probability and the value of relevant outcomes. In this paper we describe various aspects of clinical decision making in general, from a descriptive as well as a normative point of view, but with a particular focus on the condition of the root-filled tooth with post-treatment disease. We review how attention to various types of uncertainties are relevant for the decision-making process. Additionally, we discuss the nature of value judgements and different concepts of health and disease which are important for understanding the complexity of the clinical decision-making process. We also refer to a set of principal rules that can guide the clinician's decision making in every-day practice in front of a case with endodontic post-treatment disease. Finally, we provide some aspects on the sometime cumbersome decision whether to go for a non-surgical or surgical method, whenever a decision on retreatment has been made.