Apoptosis plays an essential role in both physiology and pathology. In the pathogenesis of inflammatory bowel diseases, disturbances of apoptosis also play an important role. Inflammatory cells (for example lymphocytes, granulocytes) in the gut wall are resistant to apoptotic stimuli and they accumulate there causing tissue damage. On the other hand, apoptotic elimination of the enterocytes is enhanced, which leads to the impairment of the gut barrier. The exact mechanisms of these phenomena are still poorly understood and they are still under investigation. The present paper summarises current knowledge in terms of the role of alterations of programmed cell death in the pathogenesis of inflammatory bowel diseases.