For a long time, autophagy was considered a nonselective pathway induced as a survival mechanism in response to cellular stresses. Over the past several years, however, it has become increasingly evident that autophagy also is a highly selective process involved in clearance of excess or dysfunctional organelles, protein aggregates and intracellular pathogens. In this introductory piece, we will briefly discuss the molecular mechanisms of selective types of autophagy and their emerging importance as a quality control to maintain cellular and organismal health, aspects that will be presented in deep in the reviews of this special issue of the International Journal of Cell Biology and highlighted by the research papers.