Autophagy is a process in which eukaryotic cells sequester and degrade cytoplasm and organelles via the lysosomal pathway. This process allows turnover of intracellular organelles, participates in the maintenance of cellular homeostasis and prevents accumulation of defective cellular structures. Increased autophagy is normally induced by environmental cues such as starvation and hormones, while excessive levels of autophagy can lead to autophagic programmed cell death (PCD), with features that differ from those of the apoptotic PCD process. Since autophagic PCD plays a key role in development, morphogenesis and regeneration in several animal taxa, identification of evolutionarily conserved components of the autophagic machinery is a basic starting point in order to unravel the role of autophagy under both physiological and pathological conditions. Here we summarize recent findings on the role of autophagy in two different invertebrate taxa, Platyhelminthes and Insects, focusing attention on two complex events occurring in those systems, namely planarian regeneration and insect metamorphosis. Both represent good models in which to investigate the process of autophagy and its relationship with other PCD mechanisms.