Autophagy was originally identified using transmission electron microscopy, and this technique is still one of the most sensitive approaches to detect and quantify the amount of autophagic structures in cells and tissues. However, identification of autophagosomes, amphisomes, and autolysosomes in transmission electron microscopy sections requires experience and caution. The purpose of this chapter is to provide guidelines for correct identification of autophagic structures by morphology in conventional transmission electron microscopy thin sections.