The relationship between phantom limb phenomena and cortical reorganization was examined in five subjects with congenital absence of an upper limb and nine traumatic amputees. Neuromagnetic source imaging revealed minimal reorganization of primary somatosensory cortex in the congenital amputees (M = 0.69 cm, SD 0.24) and the traumatic amputees without phantom limb pain (M = 0.27 cm, SD 0.25); the amputees with phantom limb pain showed massive cortical reorganization (M = 2.22, cm, SD 0.78). Phantom limb pain and nonpainful phantom limb phenomena were absent in the congenital amputees. Whereas phantom limb pain was positively related to cortical reorganization (r = 0.87), nonpainful phantom phenomena were not significantly correlated with cortical reorganization (r = 0.34). Sensory discrimination was normal and mislocalization (referral of stimulation-induced sensation to a phantom limb) was absent in the congenital amputees. The role of peripheral and central factors in the understanding of phantom limb pain and phantom limb phenomena is discussed in view of these findings.