Native Dancer was bred by Alfred G. Vanderbilt, Jr. and raced for him as a homebred. He was foaled at Scott Farm near Lexington, Kentucky but was raised at Vanderbilt's Sagamore Farm in Glyndon, Maryland, and is generally considered a Maryland-bred. Native Dancer was sired by the 1945 Preakness Stakes winner, Polynesian, who was otherwise known as a sprinter. His dam Geisha won only once in her eleven starts and produced no other stakes winners, though her daughter Orientation became a multiple stakes producer. Geisha was sired by Discovery, an outstanding distance horse and weight-carrier. Discovery was also the broodmare sire of leading sire Bold Ruler.