Protozoan parasites are responsible for an impressive disease burden in developing and less-developed countries. The development of vaccines and effective new therapies for dealing with these organisms are among the main gaps to be filled in the control of protozoan parasite diseases. Programmed cell death (PCD) pathways have gained attention in recent years because they comprise complex signalling pathways that can be explored for therapeutic developments. In addition, high-resolution proteomics approaches offer the opportunity to determine protein patterns associated with either cell survival or cell death. This review will focus on proteomics studies of PCD mechanisms during host-protozoan parasite interactions.