Autophagy is a bulk cytosolic degradative process which in the last few years has become a key pathway for the advancement of molecular medicine. Autophagy (cellular self-eating) has several implications in human disorders involving accumulation of cytosolic protein aggregates such as Alzheimer, Parkinson, Huntington diseases, as well as in myopathies caused by deficient lysosomal functions and in cancer. Moreover, autophagy affects intracellular microorganism lifespan, acting either as a cellular defense mechanism or, on the contrary, promoting pathogen replication. Furthermore, autophagy also participates in antigen presentation, as a part of the adaptive immune response. Therefore, autophagy association with cell survival or cell death would depend on cell nutrition conditions, presence of cell intruders, and alterations in oncogene or suppressor gene expression. In this review we will focus on the wide spectra of disease-related topics where autophagy is involved, particularly, in those processes concerning microorganism infections.