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Autophagy, the cellular machinery for targeting intracellular components for lysosomal degradation, is critically involved in the host defence to pathogenic microorganisms. Recent studies have unveiled several aspects of the immune response that are regulated by autophagy, including antigen presentation and production of proinflammatory cytokines. Polymorphisms in autophagy genes result in dysregulation of these processes and affect gut homeostasis. Genetic variants in autophagy genes are associated with Crohn's disease (CD), a disease in which an overwhelming cytokine production induces inflammation on the one hand, while a defective antigen presentation is also found on the other hand. This review summarizes the recent advances in understanding the complex interaction between innate immunity pathways and autophagy, with a focus on the modulatory effects of autophagy on inflammation.