We report a sporadic large-scale mitochondrial deletion in a paediatric patient with Fanconi's syndrome. Renal biopsy disclosed chronic interstitial nephritis. Ultrastructural examination of the renal tissue showed many giant atypical mitochondria. Histochemical stains revealed markedly reduced cytochrome c oxidase (COX). Genetic analysis disclosed a novel mitochondrial deletion of 7.3 kb in both peripheral blood and renal tissue. Mitochondrial diseases have heterogeneous clinical phenotypes; mutation analysis has proved to be an effective tool in confirming the diagnosis.