Popliteal pterygium syndrome is a condition characterized by skin webs on the popliteal fossa, which may impair mobility unless surgically repaired. Affected individuals may also have syndactyly on the fingers and/or toes. Most people with this disorder present cleft lip and cleft palate and they can have syngnathia, that is a congenital adhesion between maxilla and mandible by fibrous bands, which affects the opening of the mouth. The case that we report is about a 2-month-old male, who presented skin webs bilaterally on the popliteal fossa, syndactyly between the IV and the V toe of the right foot and between the III and the IV toe of the left foot, and genital malformations. He was born with complete bilateral cleft lip and complete cleft palate on the left side and incomplete cleft palate on the right side and syngnathia with 4 fibrous bands between the mandibular arch and the maxilla arch on the right side, which affected the opening of the mouth. The case of our patient is very interesting because there have been few reported patients affected by popliteal pterygium syndrome with syngnathia.