Abstract Short stature and failure to thrive are among the most common reasons for referral to pediatric endocrinologists. The etiology could be endocrine, genetic, nutritional, psychological, or a systemic disease. Genetic syndromes account for about 5 % of short stature in childhood. However, with increased use of genomic technologies in clinical diagnosis, the number of genes associated with short stature and failure to thrive is increasing. Some of the genetic syndromes such as Silver–Russell syndrome is clinically recognizable, while others may present as isolated short stature. We recently found ANKS1B intragenic deletion in a child with short stature, failure to thrive, and subtle distinct physical features, who was referred to us for evaluation of Silver–Russell or other genetic syndromes associated with short stature. ANKS1B is associated with neurodevelopmental disorders. However, animal study and genetic association studies suggest its role in somatic growth as well. Our observations suggest that ANKS1B is a potential candidate gene for short stature and failure to thrive in children.