Czech dysplasia, metatarsal type is an autosomal dominant skeletal disorder that is characterized by early-onset, progressive arthritis, brachydactyly of the 3rd and 4th toes, and characteristic radiographic findings in patients of normal stature. Patients with Czech dysplasia typically present in late childhood or later. In the present report, whole exome sequencing identified a mutation in COL2A1 (c.823C>T, p.R275C) known to be associated with Czech dysplasia in a 3.5 year old female who had a family history of early-onset arthritis and who was asymptomatic except for prominent knees. The use of whole exome sequencing facilitated diagnosis of this rare disease (less than 15 families in the literature) in the presymptomatic period and thus enabled us to provide early anticipatory guidance and genetic counseling for the family.