Inflammation is a key homeostatic process elicited by microbial components and by tissue damage. Increasing evidence indicates that the outcomes either tissue repair or persistent inflammatory damage and degeneration tightly depend on the pattern of cell death in situ and on infiltrating leukocytes and antigen presenting cells. Defects in the initiation and execution steps of programmed cell death such as in the clearance of cell debris are indeed often associated to inflammation defective repair and autoimmunity. Here we report recent developments on the control of apoptosis induction and execution discussing how cell death may be exploited for therapeutic purposes and the links between cell death persisting inflammation and stem cell recruitment and activation in experimental models of complex human diseases such as muscular dystrophy and cancer.