This study describes ciliated, nonciliated and mitochondrial luminal epithelial cells of the isthmus in laying and moulting domestic fowls using histological and ultrastructural techniques. The ciliated cells were nonsecretory, while numerous electron‐dense secretory granules were present in the nonciliated cells of laying birds. Mitochondrial cells, occurring in two morphologically distinct forms, constituted the third type of epithelial cell present in the isthmus. The SEM study showed that the luminal epithelium was dominated by ciliated cells, the cilia of which partially obscured adjacent nonciliated cells. The involution of the luminal epithelium in moulting birds occurred via autophagy, apoptosis and necrosis. Autophagic inclusions, which included autophagosomes and autolysosomes, were present in the early degenerative phases of ciliated, nonciliated and mitochondrial cells. Nonciliated cells underwent degeneration via apoptosis, which was characterized by nuclear and cytoplasmic condensation. Apoptotic and necrotic ciliated cells were evident during the intermediate and advanced stages of regression. The presence of apoptotic cell death was confirmed using the TUNEL assay. Loss of cilia via the formation of cilia packets was observed using TEM and SEM. Necrotic cell death occurred in mitochondrial cells during the intermediate and late stages of degeneration. In conclusion, the findings of the study on isthmus involution in moulting birds suggest that autophagy is a process confined to the early stages of degeneration, while apoptosis and/or necrosis occur in the terminal stages of regression.