Hypomelanosis of Ito (incontinentia pigmenti type I) was first described as a disorder characterized by unusual unilateral or bilateral cutaneous macular hypopigmented whorls, streaks and patches. Subsequently, neurologic, skeletal and ocular involvement were described. Kidney involvement has been reported only exceptionally. Here, we describe the case of a male infant with hypomelanosis of Ito with a prenatal diagnosis of bilateral enlargement of the kidneys, decreased corticomedullary differentiation and cysts located in the cortical and subcapsular regions. These findings were confirmed postnatally. The skin examination showed hypopigmented linear and round diffuse lesions located on the right leg and the arms. Ophthalmological examination showed anterior capsular and posterior subcapsular cataract of the left eye. Renal biopsy was characteristic of glomerulocystic kidney disease, whereas the skin biopsy confirmed the clinical diagnosis of hypomelanosis of Ito. Four other cases of kidney disease in hypomelanosis of Ito have been reported, including two cases characterized by cystic renal changes, indicating that gene abnormalities that cause hypomelanosis of Ito may also impair normal renal development, causing renal cystic changes.