Background The corticospinal tract has a sequential development in which the ipsilateral projections are gradually withdrawn, whereas the contralateral projections persist. A unilateral lesion in the motor cortex during early life may cause a reorganization in this process with preservation of uncrossed corticospinal connections in the spared hemisphere. As a result, all the motor function is lateralized in one hemisphere. Individuals with this kind of lesions also have an increased risk of drug-resistant epilepsy and may be candidates for epilepsy surgery. In these cases, it is important to evaluate the motor function for surgical treatment. Material and methods We present a series of 4 patients with pharmacoresistant epilepsy and early-life primary motor cortex lesion that were studied for epilepsy surgery. We used nTMS to investigate if there was still functional motor activity in one or both frontal cortices. Results In three cases there was no activity in the pathological cortex obtaining a bilateral response in the normal cortex. Two of them underwent fMRI using a motor task showing bilateral motor cortical function in one patient, and unilateral activation of ipsilateral motor cortex in the other patient. The last patient showed a crossed response. Two patients were operated without new postoperative deficits. Conclusions nTMS helps to define unusual lateralization of motor cortex and to guide a secure resection with the least motor deficits.