Autophagy is a catabolic process that involves the degradation of cellular components through the lysosomal machinery, re-locating nutrients from unnecessary processes to more pivotal processes required for survival. It has been reported that systemic disruption of Atg5 gene, a component of autophagy, is lethal, and that its tissue-specific disruption causes tissue degeneration in several organs. However, the functional significance of autophagy in the thyroid glands remained unknown. Therefore, we evaluated (i) hormonal regulation of autophagy in the thyroid, and (ii) the consequence of Atg5 gene knockout in the thyroid morphology and function. First, TSH-regulation of autophagy was evaluated in rat thyroid PCCL3 cells and mice. We found an increase in LC3-II puncta by TSH stimulation, demonstrating TSH-induction of autophagy. Second, Atg5flox/flox mice were crossed with TPO-Cre mice, yielding the thyroid follicular epithelial cell (thyrocyte)-specific ATG5 deficient mic (Atg5thyr-KO/KO). Atg5 gene knockout was confirmed by a lack of ATG5 expression, and disruption of autophagy was demonstrated by a decrease in LC3-II puncta and an increase in p62. Atg5thyr-KO/KO mice were born normally, and thyroid morphology, thyroid weights, and serum T4 and TSH levels were almost normal at 4 months. However, at 8 and 12 months, although thyroid function was still normal, a decrease in the number of thyrocytes, and an increase in TUNEL+-thyrocytes (i.e., apoptotic cells) were observed in Atg5thyr-KO/KO mice. Number of irregularly shaped follicles (gourd-shaped) was also increased. Excess oxidative stress was indicated by increased 8-OHdG and 53BP1 foci in Atg5thyr-KO/KO mice. These data demonstrate that (i) thyrocytes gradually undergo degradation/cell death in the absence of basal levels of autophagy, indicating that autophagy is critical for the quality control of thyrocytes, and (ii) TSH stimulates autophagy, probably by responding to increased nutritional demand required for TSH-induced cell proliferation