OBJECTIVES: To investigate variations in the autonomic functions and blood-flow velocity of the arteries supplying to the brainstem in supine and prone positions. METHODS: Forty-one full-term infants were studied at the age of 24-72 h. Each infant underwent respiratory, cardiac and eye movement analyses in supine and prone positions. In addition, blood-flow velocity of the basilar and vertebral arteries was measured with a 2 MHz probe for 5 min in each position. Two time domain measures of heart rate variability (HRV) (Standard deviation of normal R-R intervals for long-term and pNN50 for short-term variability) were employed. RESULTS: Significantly decreased short- (P<0.001) and long (P = 0.003)-term variabilities were observed in prone when compared with supine position. Increased short-term variability in active sleep with no interaction with position was observed (P = 0.005). A significant decreased mean (P = 0.001) and peak (P = 0.001-0.003) blood-flow velocity in prone when compared with supine position were measured in all three arteries supplying to the brainstem. No significant correlation between HRV and arterial blood-flow velocity (ABFV) was observed in either position. COMMENT: The results of the present study in agreement with previous studies reflect the vulnerability of infants in prone position as related to brainstem function. However, it appears that ABFV and autonomic functions as reflected by HRV are independent physiological measures, possibly indicating regulation autonomy of the central nervous system.