To examine the correlation between a clinical measure of function in patients undergoing rehabilitation who had recently had an ischemic stroke and to examine cardiophysiologic measures registered during effort. A cohort study comprising a sample of consecutive patients, without a history of cardiac disease or rhythm disturbances, admitted for rehabilitation after an ischemic supratentorial stroke. All patients were examined for the FIM trade mark score and dynamic cardiophysiologic variables. Results were analyzed in relation to stroke location. Thirty-eight patients participated in the study. Ten patients had a superficial lesion, 20 had a deep brain lesion, and eight had no noticeable lesion by computed tomographic imaging. Function was measured with the FIM instrument 48-72 hr after admission and repeated at 1 wk before discharge. Electrocardiographic activity was recorded during physiotherapy treatment. The relationship between the RR and QT intervals in the electrocardiographic waveforms was found to estimate two cardiophysiologic variables, the constant (a) and the slope (b) values, reflecting the dynamic change of QT during physiotherapy effort. Only for the subgroup of patients who sustained a deep brain lesion did the motor items in the FIM instrument on admission and discharge scores have a statistically significant relationship with the slope variable (b) and an inverse statistically significant relationship with the constant variable (a). Deep brain infarction seems to result in a significant dysfunction of the autonomic nervous system, manifesting itself as distorted dynamic behavior of the QT interval and with impaired functional performance.