3-methylglutaconic aciduria is frequently found during urine organic acid analysis and is widely regarded as a marker of a mitochondrial disorder, the clinical features of which are very heterogeneous. We describe two siblings with 3-methylglutaconic aciduria in whom renal ultrasonography showed echogenic medullae consistent with nephrocalcinosis. One patient also developed medullary cysts. In both children renal function was normal and neither had any plasma or urinary evidence of tubulopathy. The presence of nephrocalcinosis and medullary cysts in patients with 3-methylglutaconic aciduria adds to the heterogeneous clinical presentation of this group of disorders.