Some features of VATER can be seen on prenatal ultrasound so that the diagnosis may be suspected at birth. Ultrasound can see differences of the vertebrae, heart, limbs, limb positions, kidneys, and some reproductive parts. Other problems that are associated with VATER on ultrasound are poor fetal growth, excessive fluid in the womb, absent or collapsed stomach, and one artery in the umbilical cord instead of the usual two. VATER features that cannot be seen on ultrasound are differences of the anus, esophagus, and trachea.

Even if VATER is suspected before birth, an infant must be examined after birth to determine the extent of features. The entire pattern of internal and external differences will determine if the infant has VATER association, another multiple birth defect syndrome, or a genetic syndrome (such as Holt-Oram syndrome, TAR syndrome, or Fanconi anemia). Since VATER overlaps with some genetic syndromes, some infants may fit the VATER pattern and still have another diagnosis. VATER only describes the pattern of related birth defects. Since the genetic causes of VATER are unknown, genetic testing is not available. A family history focusing on VATER features can help to determine if an infant has a sporadic case or a rare inherited case.