Polydactyly is due to an error in the process of fetal developement. It is caused by an autosomal dominant gene. This means that since the gene is autosomal (not sex-linked), males and females are equally likely to inherit the trait. This also means that since the gene is dominant, children who have only one parent with the trait have a 50% chance of inheriting it. However, people in the same family carrying the same gene can have different degrees of polydactyly. Polydactyly and syndactyly are also possible outcomes of a large number of rare inherited and developmental disorders.

For example, polydactyly is a characteristic of Meckel syndrome and Laurence-Moon-Biedl syndrome. Polydactyly may also be present in Patau's syndrome, asphyxiating thoracic dystrophy, hereditary spherocytic hemolytic anemia, Moebius syndrome, VACTERL association, and Klippel-Trenaunay syndrome.

In some isolated cases of polydactyly is not possible to determine the cause. Some of these cases might nevertheless be due to genetic defects; sometimes there is too little information to demonstrate a genetic cause. Some cases might be due to external factors like exposure to toxins or womb anomalies.