The exact genetic cause of VATER association is unknown. Most cases are sporadic and do not occur more than once in the same family. This was determined by studies of families with an affected individual. Since cases are rare and most are isolated in a family, studies to find a genetic cause have been unsuccessful. Parents of a child with VATER association have a 1% or less chance of having another baby with the same condition. There have been a few reports of affected individuals with a parent or sibling showing a single feature of the VATER spectrum. There has only been one reported case of a parent and child both affected with multiple VATER features.

Most individuals with VATER association have a normal chromosome pattern. However, a few cases of chromosome differences have been reported in individuals with VATER. One child with VATER had a deletion (missing piece) on the long arm of chromosome 6. Another male infant had a deletion on the long arm of chromosome 13. There have been other children reported with a chromosome 13 deletion and VATER-like features. This infant was the first reported with the deletion to have all of the VACTERL main features. He was also the first with this chromosome deletion to have a connection between his trachea and esophagus. Another child with VATER association had an extra marker chromosome. This is a fragment of chromosomal material present in the cell in addition to the usual 46 chromosomes. This child's marker was found to contain material from chromosome 12. These cases have not led to the discovery of a gene involved in VATER.