The Prisoner’s Dilemma (PD) is one of the most popular concepts amongst the scientific literature. The task is used in order to study different types of social interactions by giving participants the choice to defect or cooperate in a specific social setting/dilemma. This review focuses on the technical characteristics of the PD task as it is used in medical literature and describes how the different PD settings could influence the players’ behaviour. We identify all the studies that have used the PD task in medical research with human participants and distinguish, following a heuristic approach, seven parameters that can differentiate a PD task, namely (a) the opponent parties’ composition; (b) the type of the opponent as perceived by the players; (c) the interaction flow of the game; (d) the number of rounds; (e) the instructions narrative and options that are given to players; (f) the strategy and (g) the reward matrix and payoffs of the game. We describe how each parameter could influence the final outcome of the PD task and highlight the great variability concerning the settings of these parameters in medical research. Our aim is to point out the heterogeneity of such methods in the past literature and to assist future researchers with their methodology design.