In this short review we attempt to establish and/or strengthen connections between probiotics administration and apoptotic pathway in gastrointestinal tract. The disturbance of apoptosis is mainly deliberated in the framework of insufficient removal of immuno-effector cells that may cause autoimmunity. In the context of the inflammatory bowel disease (IBD) and necrotizing enterocolitis (NEC), the commensal bacteria and their products effect on gut and immune cell survival are illustrated. The multitude of mechanisms of probiotics to induce cell death is shortly summarized and some aspects of it are being discussed in greater detail. The mechanism of intestinal cell death induced by probiotic administration and its influence on the immune system and potential benefits of apoptosis induction during probiotic therapy is indicated.