Short-chain acylCoA dehydrogenase (SCAD) deficiency is a rare mitochondrial disorder involving the β-oxidation of fatty acylCoA compounds in chains of 4–6 carbons. Unlike other mitochondrial disorders, cases involving autoimmune diseases have not been described. We report a 15-year-old boy with SCAD deficiency who suffered from pernicious anaemia, vitiligo, scleroatrophic lichen and autoimmune thyroiditis. As has been reported in other mitochondrial disorders, we hypothesised that autoimmune diseases are also present in SCAD deficiency. Furthermore, we discuss the possible pathogenetic relationship between these diseases.