Complex painful reflex syndrome is sometimes described in the chronic phase of stroke. Acute autonomic dysfunction (AAD), which is occasionally present in cases of acute stroke, has not been studied prospectively. The aim of the study was to investigate AAD on the hemibody contralateral to the lesion in the acute phase of stroke. One hundred consecutive patients (median age ± interquartile range, 74 ± 21; range 19–93; 51 women: 80 ± 17 and 49 men: 70 ± 17 years) in the acute phase of stroke were studied prospectively. Changes in skin temperature or coloration, diaphoresis, pain, or edema were noted in the first 3 days post-stroke. Associations between AAD and topography (cortical pre- and/or post-central, insular, corona radiata, basal ganglia, internal capsule, thalamus, and brainstem), age, gender, ischemic or hemorrhagic etiology, or the presence of sensorimotor deficits or ataxia were examined using the chi-squared or Fisher's exact test and logistic regression analysis. AAD was found in 71% of the patients and showed a significant positive association with the presence of a lesion in the post-central cortex (P = 0.037), internal capsule (P = 0.005), basal ganglia (P = 0.002), or insula (P = 0.011) and a negative association with the presence of a lesion in the brainstem (P = 0.004). Multivariate logistic regression analysis including all studied topographic variables showed that only brainstem lesions were significantly associated with a decreased risk of developing AAD (odds ratio = 0.08, 95% confidence interval: 0.01–0.69, P = 0.022). AAD was not associated with age, gender, the ischemic or hemorrhagic nature of the lesion, the side of lesion, hypertonic or hypotonic paresis, or hyperreflexia or hyporeflexia. AAD was found in association with sensory deficits (P = 0.001) and contralateral hyperkinesia (P = 0.004). Acute AAD is significantly more likely to occur in the presence of hemispheric lesions involving sensory pathways from the cortex to the internal capsule and insula and is significantly less prevalent in the presence of brainstem lesions.