Autophagy is a homeostatic mechanism for the catabolism of cytosolic constituents, including organelles, in times of stress and nutrient deprivation. In addition, autophagy has been linked to innate and adaptive immune responses to numerous infectious microorganisms, including mycobacteria. This review explores the role of autophagy in the responses of antigen-presenting cells to mycobacteria, including links with phagosome maturation, inflammasome activation and antigen presentation. In addition, the modulation of autophagy by cytokines and pathogen-derived stimuli is discussed.