Cystinosis is an autosomal recessive lysosomal storage disorder characterized by the accumulation of the amino-acid cysteine in various organs and tissues. Infantile nephropathic cystinosis is the most severe form of the disorder. We describe the clinical features in a four and a half-year-old Indian boy with infantile nephropathic cystinosis that presented with the incomplete Fanconi syndrome, hydro-uretero-nephrosis with megacystis, and hypothyroidism.