Recently, several groups made a nearly simultaneous discovery that autophagic degradation represents a previously unrecognized effector of innate and adaptive immunity. Despite the fact that hints to these phenomena hail back to earlier sporadic reports, autophagy has, until now, received attention primarily as a fundamental cellular homeostasis pathway, whereby cytoplasm portions get sequestered by the membrane for delivery to lysosomes. This process leads to the removal of damaged or surplus organelles and digests stable, long-lived macromolecules. Autophagy has been implicated previously in both health-promoting and disease-associated states, in cancer, neurodegeneration, development and aging. A protective role has recently been demonstrated in infectious diseases, which represents a previously unrecognized immune mechanism acting against intracellular microbes. This review reviews autophagy as an immune mechanism.