Current evidence implicates autophagy in the regulation of lipid stores within the two main organs involved in maintaining lipid homeostasis, the liver and adipose tissue. Critical to this role in hepatocytes is the breakdown of cytoplasmic lipid droplets, a process referred to as lipophagy. Conversely, autophagy is required for adipocyte differentiation and the concurrent accumulation of lipid droplets. Autophagy also affects lipid metabolism through contributions to lipoprotein assembly. A number of reports have now implicated autophagy in the degradation of apolipoprotein B, the main structural protein of very-low-density-lipoprotein. Aberrant autophagy may also be involved in conditions of deregulated lipid homeostasis in metabolic disorders such as the metabolic syndrome. First, insulin signalling and autophagy activity appear to diverge in a mechanism of reciprocal regulation, suggesting a role for autophagy in insulin resistance. Secondly, upregulation of autophagy may lead to conversion of white adipose tissue into brown adipose tissue, thus regulating energy expenditure and obesity. Thirdly, upregulation of autophagy in hepatocytes could increase breakdown of lipid stores controlling triglyceride homeostasis and fatty liver. Taken together, autophagy appears to play a very complex role in lipid homeostasis, affecting lipid stores differently depending on the tissue, as well as contributing to pathways of lipoprotein metabolism.