The kabuki make-up syndrome is characterized by peculiar facies, skeletal anomalies, abnormal dermatoglyphics, mental retardation and postnatal growth failure. Until 1988, 62 cases had been reported and 50 (81%) of them had short stature. However, the cause of short stature has not been elucidated, while one case had growth hormone (GH) deficiency. We report another case of growth hormone deficiency associated with abonormal brain magnetic resonance (MR) imaging findings which were characterized by a non-visualized pituitary stalk, atrophic anterior pituitary gland and ectopic posterior lobe. However, this case had no notable perinatal history but had a cleft palate. Therefore, the GH deficiency in this case might have been caused by hypothalamo-pituitary dysgenesis, i. e. a part of a series of midline anomalies.