The effect of peripheral lesions on cerebral somatosensory representations is well studied for experimentally induced amputations and deafferentations acquired later in life. However, few studies have investigated the brain's capacity for plastic changes in congenital malformations. We studied somatosensory evoked fields to electrical stimulation of the bordering fingers in 10 subjects with upper extremity dysmelia in comparison to 10 control subjects using a 122-channal whole-head magnetometer. The number of developed fingers varied between two and four in the affected subjects. We localized finger representations in the primary somatosensory cortex and calculated Euclidian distances to estimate the size of the somatosensory hand area. Euclidian distances were significantly smaller in dysmelic subjects (5.7 mm) than in control subjects (11.6 mm) and were related to the number of the developed fingers on the contralateral hand. In contrast, individual finger representations were not found to be reduced. We suggest that the shrinkage of the somatosensory hand area might be related to the congenital nature of the malformation, to the smaller anatomical hand size in the affected subjects and/or to use-dependent effects due to impaired hand function.