Autophagy is a conservative evolutionary established cellular process functioning to maintain cell homeostasis. Furthermore, the cellular autophagy program acts as the primary mechanism of intracellular defense in the cells infected with viruses or other pathogens. However, many viruses are able to modulate the cellular autophagy program by induction or inhibition its individual stages through various mechanisms. Autophagy can function both, as proviral and antiviral mechanism, in the pathogenesis of infection depending on the virus and cell type. This review discusses relevant studies of the mechanisms of interaction between the cellular program of autophagy and viral replication, in particular, flaviviruses, paramyxoviruses, coronaviruses and others. The study of these mechanisms may be important for a better understanding of the pathogenesis of viral infectious diseases and the identification of new therapeutic targets.