Dying epithelial cells are thought to be squeezed out of the epithelium by the contraction of an actomyosin ring formed in live neighboring cells, which simultaneously closes any potential gap, thereby maintaining the integrity of the epithelial layer. The shrinkage and contraction of apoptotic cells contribute little to the extrusion process. In contrast, the clearance of dying intestinal columnar epithelial cells in vivo usually leaves a transient gap via an unknown mechanism. By using freshly isolated small intestinal villus units with or without basal lamina, we found that the nucleus of apoptotic enterocytes moved apically until they budded off, leaving the cytoplasmic residue in the transient gap. Apical polarity of nucleus movement was restricted unless the basal lamina was artificially removed. F-actin mainly accumulated in apoptotic cells rather than neighboring live cells, even after the addition of resistance force against extrusion. The actin accumulation in apoptotic cells does not depend on the living state of neighboring cells. Apoptotic cells can complete the shedding process when neighboring a goblet cell, as the majority of space is occupied by mucin granules and the cytoplasm consists of intermediate filaments and microtubules, but lacks F-actin. We found that the elongation and deformation of apoptotic cells depend on the stretching force generated inside the cell, rather than the force generated by neighboring cells extending. Our findings clearly demonstrate that intestinal epithelial shedding does not depend on the formation and contraction of an actomyosin ring in live neighboring cells. Apoptotic epithelial cells may undergo an active process of cell deformation with adhesion-restricted polarity, which may contribute to maintaining barrier function during a high rate of cellular turnover.