BACKGROUND AND PURPOSE: Heart rate variability (HRV) as a measure of autonomic function might provide prognostic information in ischemic stroke. However, numerous difficulties are associated with HRV parameters assessment and interpretation, especially in short-term ECG recordings. For better understanding of derived HRV data and to avoid methodological bias we simultaneously recorded and analyzed heart rate, blood pressure and respiratory rate. METHODS: Seventy-five ischemic stroke patients underwent short-term ECG recordings. Linear and nonlinear parameters of HRV as well as beat-to-beat blood pressure and respiratory rate were assessed and compared in patients with different functional neurological outcomes at 7th and 90th days. RESULTS: Values of Approximate, Sample and Fuzzy Entropy were significantly lower in patients with poor early neurological outcome. Patients with poor 90-day outcome had higher percentage of high frequency spectrum and normalized high frequency power, lower normalized low frequency power and lower low frequency/high frequency ratio. Low frequency/high frequency ratio correlated negatively with scores in the National Institutes of Health Stroke Scale and modified Rankin Scale (mRS) at the 7th and mRS at the 90th days. Mean RR interval, values of blood pressure as well as blood pressure variability did not differ between groups with good and poor outcomes. Respiratory frequency was significantly correlated with the functional neurological outcome at 7th and 90th days. CONCLUSION: While HRV assessed by linear methods seems to have long-term prognostic value, complexity measures of HRV reflect the impact of the neurological state on distinct, temporary properties of heart rate dynamic. Respiratory rate during the first days of the stroke is associated with early and long-term neurological outcome and should be further investigated as a potential risk factor.