Bilateral basal ganglia lesions are a common non-specific finding seen in many diseases. One of the differential diagnoses for it, in a child, is kernicterus occurring due to hyperbilirubinemia. Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common cause of severe hyperbilirubinemia. A 1-year old child presented to the hospital with history of generalized dystonia in the previous 3 days. MRI showed evidence of symmetrical lesions in bilateral globus pallidus, which were hyperintense on T2/FLAIR and isointense on T1. Patient’s blood test revealed G6PD deficiency. Hence, a diagnosis of G6PD deficiency leading to kernicterus was made. In a child, the diseases that may affect the basal ganglia symmetrically and bilaterally include kernicterus, hypoxia, carbon monoxide poisoning, hypoglycemia, inherited metabolic and dysmyelinating disorders like Leigh disorder, Canavan and Krabbe, Neurofibromatosis, Herpes encephalitis, congenital HIV infection, manganese poisoning and extrapontine myelinolysis. Important causes of kernicterus are Rh incompatibility, ABO incompatibility, sepsis, hemolytic anaemia and G6PD deficiency. G6PD deficiency leading to kernicterus should be considered a differential diagnosis of bilateral basal ganglia lesions in children. Proper elicitation of history with appropriate blood biochemical tests will help in arriving at a proper diagnosis.