The aim of this study was to assess the activation of primary motor cortex, prefrontal cortex and parietal cortex during simple and complex motor tasks performed with the hemiparetic and non-hemiparetic hand. Seven patients after stroke in the left brain hemisphere were included in the study. Functional magnetic resonance imaging (fMRI) was performed in the first and third week, and in three patients also three months after the stroke. Performance of both the simple and the complex tasks with the hemiparetic or non-hemiparetic hand resulted in activations of the motor cortex, prefrontal cortex and parietal cortex in majority of the consecutive fMRI sessions. Three months after the stroke fMRI data reveled reduced activation of primary motor cortex and parietal cortex in the contralesional hemisphere during the performance of the simple task by the hemiparetic hand. During the complex task, the reduction of activation was less prominent. Results of the present study suggest that in mildly impaired stroke patients a bilateral activation of prefrontal and parietal cortex may participate in the recovery process from stroke. The potential for measurement of cortical rehabilitation is discussed.