Abstract: Objectives To analyze a rare autosomal recessive disease, aggrecan type spondylometaphyseal dysplasia (SEMD), which was caused by ACAN gene mutations. Methods A 7 years old girl was diagnosed with short stature after excluding growth hormone deficiency, idiopathic short stature, and hypothyroidism. Combining family history and clinical features, SEMD were suspected and genetic tests were performed. Results The patient was found with homozygous mutations of c.512C > T in ACAN gene, and was diagnosed with aggrecan type SEMD. Her parents were found to be heterozygous mutation carrier. Conclusions In patients with high suspection of a special type of short stature, early genetic tests should be carried out for a clear diagnosis.