Achondroplasia is caused by a gene alteration (mutation) in the FGFR3 gene. The FGFR3 gene makes a protein called fibroblast growth factor receptor 3 that is involved in converting cartilage to bone. FGFR3 is the only gene known to be associated with achondroplasia. All people who have only a single copy of the normal FGFR3 gene and a single copy of the FGFR3 gene mutation have achondroplasia.

Most people who have achondroplasia have average-size parents. In this situation, the FGFR3 gene mutation occurs in one parent's egg or sperm cell before conception. Other people with achondroplasia inherit the condition from a parent who has achondroplasia.