Significant effort has been placed on developing decision support tools to improve patient care. However, drivers of real-world clinical decisions in complex medical scenarios are not yet well-understood, resulting in substantial gaps between these tools and practical applications. In light of this, we highlight that more attention on understanding clinical decision-making is required both to elucidate current clinical practices and to enable effective human-machine interactions. This is imperative in high-stakes scenarios with scarce available resources. Using organ transplantation as a case study, we formalize the desiderata of methods for understanding clinical decision-making. We show that most existing machine learning methods are insufficient to meet these requirements and propose iTransplant, a novel data-driven framework to learn the factors affecting decisions on organ offers in an instance-wise fashion directly from clinical data, as a possible solution. Through experiments on real-world liver transplantation data from OPTN, we demonstrate the use of iTransplant to: (1) discover which criteria are most important to clinicians for organ offer acceptance; (2) identify patient-specific organ preferences of clinicians allowing automatic patient stratification; and (3) explore variations in transplantation practices between different transplant centers. Finally, we emphasize that the insights gained by iTransplant can be used to inform the development of future decision support tools.