Dysfunction of the autonomic nervous system (ANS) often complicates the clinical course in patients with acute stroke. The studies of the function of ANS in patients with brainstem stroke are scarce. The purpose of our study was to evaluate the function of ANS in the early period after acute brainstem stroke and to find out whether the location of stroke in brainstem influences the function of ANS. We studied heart rate variability (HRV) and plasma levels of catecholamines in 14 eligible patients with medullary (6 patients) and non-medullary (8 patients) brainstem stroke during the first 6 weeks after stroke. Integrals over the low- (LFB; 0.04-0.15 Hz) and high-frequency bands (HFB; 0.15-0.40 Hz) of power spectra were calculated. When compared to controls, the integrals over HFB in the hyperacute (p < 0.001) and over LFB in the hyperacute (p < 0.005) and in the acute (p < 0.05) phases were significantly smaller in patients with medullary strokes. Integrals over LFB and HFB in patients with non-medullary strokes did not differ significantly from controls, regardless of the phase of the disease. Plasma levels of epinephrine in patients with non-medullary stroke in the hyperacute and in the acute phases were significantly higher than in controls (p < 0.005). We conclude that there is transient dysfunction of ANS in patients with acute medullary stroke, in contrast to those with non-medullary brainstem stroke.