Even though the medulla contains the baroreceptor regulatory centers, few studies have focused on the autonomic dysfunction of lateral medullary infarction (LMI). Therefore, cardiac parasympathetic and sympathetic functions were compared in LMI patients and age-matched controls. We prospectively recruited 25 LMI patients who had ipsilateral Horner's sign and cardiac autonomic function testing without a history of diabetes, cardiac disease, or previous stroke. Parasympathetic function tests included beat-to-beat heart rate variation during deep breathing, 30:15 heart rate ratio testing while standing, and the valsalva ratio. Sympathetic function tests included blood pressure during active standing and sustained handgrip. The composite autonomic score (CAS) was measured as a total of 10 points; parasympathetic dysfunction was designated as ≥3 points in the parasympathetic subscores and sympathetic dysfunction as ≥2 points in the sympathetic subscores. Multiple regression analysis was performed to predict parasympathetic or sympathetic dysfunction. The mean age and stroke risk factors of the study population were not significantly different between the LMI group (n = 25) and control group (n = 29). However, cardiac autonomic functions were significantly different in the groups: parasympathetic dysfunction (14 vs. 4 patients, p = 0.011) and sympathetic dysfunction (3 vs. 13 patients, p = 0.008). In univariate analysis, male-gender (p = 0.011), right-side involvement (p = 0.035) and ventral involvement (p = 0.007) were significantly associated with parasympathetic dysfunction (CAS subscore ≥3). In multivariable analysis, the ventral involvement remained to be the independent predictor for parasympathetic dysfunction (OR 16.0; 95% CI 2.2-118.3, p = 0.007). This study suggests that LMI patients are susceptible to cardiac parasympathetic dysfunction, especially in the ventral medulla.