It is widely believed that people who are congenitally limb-deficient or suffer a limb amputation at an early age do not experience phantom limbs. The present study reports on a sample of 125 people with missing limbs and documents phantom experiences in 41 individuals who were either born limb-deficient (n = 15) or underwent amputation before the age of 6 years (n = 26). These cases provide evidence that phantom limbs are experienced by at least 20% of congenitally limb-deficient subjects and by 50% of subjects who underwent amputations before the age of 6 years. The phantoms are detailed and can be described in terms of size, shape, position, movement and temporal properties. The perceptual qualities of the phantoms can also be described by sensory descriptors and are reported as painful by 20% of subjects with phantoms in the congenital limb deficient group and 42% of young amputees. It is argued that these phantom experiences provide evidence of a distributed neural representation of the body that is in part genetically determined.