This review summarizes the current methods for monitoring and measuring autophagy, a cellular process that degrades cytoplasmic components and is crucial for cellular homeostasis and survival under stress. Autophagy can be categorized into three types: macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA). The review focuses on methods to identify autophagic structures and measure autophagic flux in cultured cells and animals, as well as existing autophagy reporter mice useful for autophagy studies and drug testing. It also discusses the challenges in monitoring autophagy in human samples. Key methods for identifying autophagic structures include electron microscopy, immunoblotting, and fluorescent protein markers such as LC3, p62, and Keima. LC3 is a widely used marker for autophagosomes, and its conversion from LC3-I to LC3-II is a key indicator of autophagic activity. p62 is another marker that is selectively degraded by autophagy. Fluorescent probes such as mRFP-GFP-LC3 and Keima are used to visualize autophagic flux and distinguish between autophagosomes and autolysosomes. To measure autophagic flux, methods include immunoblotting, fluorescence microscopy, and flow cytometry. These methods assess the degradation of autophagic substrates and the turnover of autophagosomes. The review also discusses the use of autophagy reporter mice, such as GFP-LC3 and mRFP-GFP-LC3 mice, to monitor autophagy in vivo. These mice allow for the visualization of autophagic structures and the assessment of autophagic flux in various tissues and organs. The review highlights the challenges in monitoring autophagy in human samples, as static analyses cannot distinguish between autophagy upregulation and degradation inhibition. Additionally, the review discusses the use of patient-derived cells to study genetic mutations that may affect autophagic flux. Overall, the review emphasizes the importance of using appropriate methods and combining multiple approaches to accurately assess autophagic activity.This review summarizes the current methods for monitoring and measuring autophagy, a cellular process that degrades cytoplasmic components and is crucial for cellular homeostasis and survival under stress. Autophagy can be categorized into three types: macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA). The review focuses on methods to identify autophagic structures and measure autophagic flux in cultured cells and animals, as well as existing autophagy reporter mice useful for autophagy studies and drug testing. It also discusses the challenges in monitoring autophagy in human samples. Key methods for identifying autophagic structures include electron microscopy, immunoblotting, and fluorescent protein markers such as LC3, p62, and Keima. LC3 is a widely used marker for autophagosomes, and its conversion from LC3-I to LC3-II is a key indicator of autophagic activity. p62 is another marker that is selectively degraded by autophagy. Fluorescent probes such as mRFP-GFP-LC3 and Keima are used to visualize autophagic flux and distinguish between autophagosomes and autolysosomes. To measure autophagic flux, methods include immunoblotting, fluorescence microscopy, and flow cytometry. These methods assess the degradation of autophagic substrates and the turnover of autophagosomes. The review also discusses the use of autophagy reporter mice, such as GFP-LC3 and mRFP-GFP-LC3 mice, to monitor autophagy in vivo. These mice allow for the visualization of autophagic structures and the assessment of autophagic flux in various tissues and organs. The review highlights the challenges in monitoring autophagy in human samples, as static analyses cannot distinguish between autophagy upregulation and degradation inhibition. Additionally, the review discusses the use of patient-derived cells to study genetic mutations that may affect autophagic flux. Overall, the review emphasizes the importance of using appropriate methods and combining multiple approaches to accurately assess autophagic activity.