The case report describes a young boy with renal, retinal, hepatic and cerebellar involvement in a rare syndrome. He had polyuria, deranged renal functions and cystic lesions in kidneys, which led to the diagnosis of nephronophthisis (NPH). Extra-renal involvement with night blindness, truncal ataxia, mental retardation and hepatosplenomegaly. Thus, every patient with NPH should be carefully examined for extra-renal involvement.