Background Rural compared to urban Thai populations have a higher incidence of sudden unexplained nocturnal death syndrome (SUNDS). This study tests the hypothesis that compared to young urban Thai men, the young rural northeast Thai men display autonomic system dysfunction that may contribute to their relatively high risk to develop SUNDS. Methods Forty-seven healthy second and third year students from Khon Kaen University (20–22 years old) were divided into central, urban northeastern, and rural northeastern groups, based on the locality in which they had grown up and in which their parents had lived prior to their birth. Results Body weight, body height, serum sodium, serum potassium, fasting blood sugar, glucose tolerance, resting mean arterial pressure, resting heart rate, ulnar nerve conduction velocity, and sympathetic and parasympathetic nervous system activity were not significantly different among the three groups. In contrast, compared to urban northeasterners and central Thais, rural northeasterners displayed low sympathetic and high parasympathetic responses to cold stress and oral saline load; however, baroreflex sensitivity and the autonomic nervous system responses to upright tilt were not significantly different among the three groups. In addition, respiratory rates at rest and in response to upright tilt, cold stress, and oral saline load were not significantly different among the three groups. Conclusions These data indicate that compared to central or urban, individuals from rural origin display decreased sympathetic and increased parasympathetic responses to stresses. These altered responses could predispose the individuals to inappropriate autonomic control during the stresses, including those resulting in SUNDS.