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Herein, we report on a paediatric patient with mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) who was hospitalized for acute on chronic renal insufficiency, seizures and deterioration of the level of consciousness. She also had hypertension, hypothyroidism and nephrotic range proteinuria. Kidney biopsy revealed many sclerotic glomeruli and focal segmental glomerulosclerosis (FSGS). Glomerulopathy is rare in patients with MELAS, and FSGS has been reported only in a few patients. The histopathological features of the renal biopsy suggested that the aetiology of the FSGS may have been secondary to chronic renal injury rather than from a primary immunologic cause. Moreover, our case is unique in that, the coexistence of MELAS, hypothalamic hypothyroidism and FSGS has not been reported in the past. The purpose of this report is to increase the awareness of health-care professionals, especially in the fields of paediatrics, neurology, endocrinology and nephrology, regarding the manifestations and complications of MELAS.