Autophagy is a cellular mechanism for the sequestration and degradation of intracellular pathogens and compromised organelles, particularly damaged mitochondria. Autophagy also clears other cellular components, such as inflammasomes and cytokines, thus providing an important means of regulating inflammation. Defects in autophagy have been found by genetic association studies to confer susceptibility to several autoimmune and inflammatory disorders, particularly inflammatory bowel disease. Thus, the manipulation of autophagy in disease situations is of growing interest for therapeutic targeting; however, the involvement of autophagy in cellular homoeostasis, in normal immune function and in inflammation is manifold. An appreciation of the intricacies of the contributions of this process to inflammation, and how these are altered by various immune and environmental stimuli, is essential for the understanding and interpretation of studies of inflammation and the design of therapeutics exploiting the manipulation of autophagy. This review focuses on the known roles of autophagy in the induction and maintenance of inflammation and on its role in the aetiology and regulation of inflammatory and autoimmune disorders.