Mitochondrial swelling has huge impact to multicellular organisms since it triggers apoptosis, the programmed cell death. In this paper we present a new mathematical model of this phenomenon. As a novelty it includes spatial effects, which are of great importance for the in vivo process. Our model considers three mitochondrial subpopulations varying in the degree of swelling. The evolution of these groups is dependent on the present calcium concentration and is described by a system of ODEs, whereas the calcium propagation is modeled by a reaction-diffusion equation taking into account spatial effects. We analyze the derived model with respect to existence and long-time behavior of solutions and obtain a complete mathematical classification of the swelling process.