The paper presents a methodology of calculating negative heat flows in the cylinder-piston group of theStirling engine. Some of the most important of them are the shuttle effect and the pumping losses. The introductorypart of the article describes the physical side of the phenomena under investigation. The main relationshipsrecommended by the researchers for the calculation of the shuttle effect and pumping losses are presented in thepaper. A mathematical model is developed for the purpose of calculating the heat losses mentioned. The model isbased on representing the phenomenon as quasistationary radial heat transfer by means of convection and radiation.A system of algebraic differential equations of heat exchange between single elements of arrays is presented.The system of the main equations is solved by a numerical method of integration (a variety of Euler method -the method of limiting overrelaxation). Algorithms of controlling the accuracy of the calculations performed areincorporated in the program of calculation. The algorithm is used for defining the level of shuttle conduction andpumping loss in the1R30/6 Stirling engine designed at Saint-Petersburg State Marine Technical University. Inaddition a methodology of finding the heat dissipation factor in the gap between the displacer and the cylinderwall was developed. The extent of influence of the engine design data on the phenomena under consideration isanalyzed. Rank diagrams are constructed that visualize the results obtained.