An epidemiological analysis of the association of polydactyly with other congenital anomalies was performed in 5,927 consecutively born polydactyly cases. They were grouped into three categories: duplicated fifth digit, duplicated first digit, and rare polydactylies; also into isolated or associated groups, if other birth defects were or were not observed in the same infant. Associated cases were further subdivided into: combined, if the other defect was a limb defect; syndromic, if a non-limb defect constituted a recognized causal or pathogenetic entity; and MCA, if a non-limb defect did not constitute a recognized entity. In 14.6% of the 5,927 polydactyly cases studied, polydactyly was not the only congenital anomaly. This associated proportion was minimal for postaxial (11.8%), intermediate for preaxial-I (20.0%), and maximal for rare polydactyly (54.9%). Duplication of the fifth toe plus syndactyly of fourth and fifth toes, as well as other syndactylies adjacent to the duplicated digit is the most frequent type. Syndactyly of fourth and fifth toes was also combined with a duplicated fifth finger, suggesting the existence of an arrested or amputated in utero sixth toe. Polydactylies are rarely associated with other congenital anomalies except in recognizable syndromes. When syndromes are excluded, most of the significant positive associations disappear. Trisomy 13, Meckel, and Down syndrome explained 255 of the 338 syndromic polydactyly cases. Down syndrome is strongly associated with first-digit duplication, and negatively associated with postaxial polydactyly. The latter could not be explained by maternal age differences among Black and non-Black case sub-sets.