A system modelling autophagy is a new area of research. Current understanding of each step in this biochemical pathway is limited. The study of this mechanism is interesting in several aspects: autophagy plays an important role in physiological cellular processes, is a survival mechanism under external stress and is also connected with cancer and neurodegenerative diseases [Cuervo, 2004; Kondo et al., 2005; Levine, 2007; Pan et al., 2008]. Autophagy is the pathway for degradation of redundant or faulty cell components. This important mechanism occurs in all eukaryotic cells as a part of cell’s everyday activities and plays an important role in cell growth and development (cellular differentiation, immunity, cellular homeostasis). This work proposes a simple mathematical model of autophagy pathway as a system with feedback, which controls the level of the total amino acid pool. Feedback comes from the amino acids which are produced during the autophagy mechanism which is induced as a result of starvation or rapamycin treatment.