Aicardi-Goutières syndrome is an early-onset encephalopathy with a presumed immune pathogenesis caused by inherited defects in nucleic acid metabolism. The clinical picture resembles a congenital viral infection despite negative investigations for common viruses. In addition to leukoencephalopathy with calcifications of basal ganglia, patients show increased levels of the antiviral cytokine interferon-α in cerebrospinal fluid. We report on a 12-year-old boy with Aicardi-Goutières syndrome and systemic lupus erythematosus (SLE) due to mutations in the SAMHD1 (sterile alpha motif domain and HD domain-containing protein 1) gene, illustrating an emerging pattern of the natural history of Aicardi-Goutières syndrome characterized by neurological disease followed by symptoms of systemic autoimmunity. Thus, Aicardi-Goutières syndrome constitutes a model disease for systemic autoimmunity triggered by the activation of the innate immune system. Recognition of the etiologic link between Aicardi-Goutières syndrome and systemic lupus erythematosus has direct implications on therapeutic management and suggests that early immune modulatory intervention can improve neurological outcome.