BACKGROUND: The level of autonomic dysbalance in the first months after acute ischemic cerebral stroke has not been thoroughly investigated, and the available data are uncomplete. The aim of this research is to establish the degree and dynamics of impaired cardiac autonomic balance recovery within the first six months following the acute ischemic cerebral stroke. METHODS: This prospective study included 78 patients who had suffered the first ischemic cerebral stroke and 78 sex and age-matched healthy subjects. We have analyzed heart rate variability (HRV) from a 24-hour Holter ECG. In the group of patients with ischemic cerebral stroke, HRV was measured after two and six months following the acute phase, respectively. RESULTS: Two and six months after the acute ischemic cerebral stroke, all HRV variables, except low to high frequency ratio (LF/HF), were significantly lower in the group of stroke patients when compared to the control group. Furthermore, we found a significant increase in the overall HRV between months 2 and 6 after the acute phase of cerebral stroke; p = 0.03 for Standard deviation of all normal R-R intervals (SDNN) and p = 0.01 for Total power. CONCLUSIONS: The results point to the gradual recovery of impaired cardiac autonomic balance in the patients with ischemic cerebral stroke within the first months following the acute phase. Nevertheless, HRV remains significantly lower even six months after the acute phase in comparison to healthy subjects.