Studies of phantom limb in cases of congenital (aplasic) absence of limb have provided inadequate evidence concerning the innate neurological substrate responsible for the phantom. In this study we review evidence from ultrasonic and behavioral studies of hand-mouth coordination in utero and in early infancy, neurobiological studies in primates, and studies of neural reorganization following amputation. We suggest two complementary hypotheses to explain aplasic phantoms. First, aplasic phantoms are based on the existence of specific neural circuitry associated with innate motor schemas, such as the neural matrix responsible for early hand-mouth coordination. Second, aplasic phantoms are modified by mechanisms that involve a reorganization of neural representations of the missing limb within a complex network involving both cortical and subcortical structures.