The measurement of motor deficits in individuals with cerebral palsy (CP) has been largely based on clinical criteria. Yet functional imaging and non-invasive stimulation methods provide a means to measure directly abnormalities of the motor system. The size and location of muscles and movement representations can be determined with transcranial magnetic stimulation (TMS) and functional magnetics resonance imaging. Thus the homunculus can be individually mapped in children with CP. Because size of representation within the homunculus relates to quality of motor control, measurement of the distance between body parts provides a metric that may be useful in classifying deficits. Bilateral motor control in one hemisphere, while normal in neonates, persists variably in CP, providing another physiological metric. In this study, we used TMS to measure hand and ankle representations in a convenience sample of children with spastic CP. Overlapping thumb and ankle maps were found in children with both hemiplegia and diplegia, and these maps may be from either side of the body. While more participants are required to make conclusions about disability and compression/bilaterality of the homunculus, it appears as if TMS-derived metrics relate to motor abnormalities. These abnormal motor maps also are a therapeutic target, as stimulation methods are being developed as adjuncts to physical means of rehabilitation.