Kleefstra or 9q subtelomeric deletion syndrome (9qSTDS) is a rare microdeletion syndrome. The most prominent phenotypic features include hypotonia, developmental retardation, as well as typical dysmorphic face. It has been shown that terminal deletions of the chromosome 9q34.3 region, or EHMT1 gene mutations, lead to Kleefstra syndrome. We present 16-month-old twin sisters, one of whom had originally been referred for Down syndrome screening due to hypotonia, growth and development retardation, dysmorphic facial signs, and accompanying congenital heart disease. They were subsequently diagnosed as Kleefstra syndrome based on subtelomeric FISH analysis. In conclusion, Kleefstra syndrome should be considered in the differential diagnosis of Down syndrome because it presents with very similar phenotypic features.