Objectives: Creatine transporter deficiency is a recently described group of disease which is an X-linked, inborn error of metabolism caused by mutations in the creatine transporter SLC6A8 gene. The common manifestations include intellectual disability, language delay, and short stature. Here, we report a novel in-frame hemizygous deletion in a boy with profound short stature and severe language delay. Purpose: The aim of this study is uncover the genetic cause of growth hormone deficiency and severe language delay. Methods: To detect a genetic cause in the patients, targeted exome sequencing was applied using the Nextseq platform and Trusight panel. Results: A 4-year old boy was referred to our hospital due to profound short stature. The patient was born at 40+3 weeks of gestation, with a birth weight of 3000 g. There was no history of perinatal distress or any significant neonatal complications. At admission, height and weight of the patient was both below the level of 2SD in same age and sex group. Mid parental height was 175.5cm. His degree of comprehensive language development is same as the level of 1.3 year old male by the measurement of Sequenced Language Scale for Infants. He was diagnosed with growth hormone deficiency by growth hormone provocation test. Chromosome and array-comparative genomic hybridization study showed all negative results. In the next step, target exome sequencing was performed in the patient resulting in in-frame hemizygous deletion, c.942_944del(p.Phe315del), on SLC6A8 which was confirmed by Sanger sequencing. MR spectroscopy showed the decreased level of creatine peak in in both parietal and right temporal lobe and urine analysis revealed significant the elevation of creatine/creatinine ratio that correspond to creatine transporter deficiency. Conclusions: This is first report on creatine transporter deficiency in a Korean population which is identified by targeted exome sequencing. Creatine transporter deficiency should be considered in the metabolic and genetic evaluation of males with profound growth delay and severe language delay.