The regeneration of the mother plant through germinative process is the main reason that evolutionarily justifies the existence of a viable seed. Current knowledge indicates that the control of germination is a sophisticated process mainly controlled by hormones and reactive oxygen species (ROS), among other endogenous factors. One of the events that directly participate in the germination is the degradation of storage proteins (SPs). Thus, vacuolar processing enzymes (VPEs) contribute to SPs' degradation and mobilization due to direct proteolysis or through the activation of other peptidases. In parallel, the relationship between VPEs and programmed cell death (PCD) is beyond doubt. As an alternative to VPEs, the formation of vesicles called ricinosomes containing papain-like Cys-proteases (PLCPs) and located in the reserve tissues of some germinating seeds also collaborates to protein degradation. Finally, there are increasing evidences linking nucleases to PCD in different tissues of seed. However, its state of the art is still little developed. Together, this current overview illustrates a part of the complexity of PCD in seeds, a puzzle far from being solved.