Aicardi-Goutières syndrome (AGS) is a rare, genetically determined encephalopathy whose importance from a clinical viewpoint is magnified because of the risk of misdiagnosis as the sequelae of congenital infection. Recent molecular advances have shown that AGS can be caused by mutations in any one of at least five genes (four of which have so far been identified), most commonly on a recessive basis but occasionally as a dominant trait. Additionally, a recent genotype-phenotype correlation has shown that two clinical presentations can be delineated; an early onset neonatal form highly reminiscent of congenital infection seen particularly with TREX1 mutations, and a later-onset presentation, sometimes occurring after several months of normal development and occasionally associated with remarkably preserved neurological function, most frequently due to RNASEH2B mutations. Evidence is emerging to show that the nucleases defective in AGS are involved in removing endogenous nucleic acid species produced during normal cellular processing, and that a failure of this removal results in inappropriate activation of the innate immune system. This hypothesis explains the phenotypic overlap of AGS with congenital infection and some aspects of systemic lupus erythematosus, where a similar interferon alpha-mediated innate immune response is triggered by viral and host nucleic acids respectively.