To assess the influence of intrauterine growth retardation and post-natal development on heart rate variability (HRV) and cardiac reflexes, we studied 27 healthy small-for-gestational age (SGA) and 23 appropriate-for-gestational age (AGA) infants during a nap study. Resting HRV was assessed by point dispersion of Poincare plots for overall (SDRR) and instantaneous beat-to-beat variability (SDRR) and the ratio (SDRR/(SDRR). Heart rate (HR) reflex and arousal responses to a 60° head-up tilt were determined. All tests/measures were repeated twice in quiet and active sleep and in prone and supine sleep positions at 1 and 3 months of age. SGA infants exhibited higher resting sympathetic tone [SDRR/(SDRR: 1.9 (95% CI: 1.7, 2.0) and 1.7 (1.5, 1.8) in SGA and AGA respectively, p = 0.046], and a tendency for a smaller tachycardic reflex response to the tilt HR: 24 (95% CI: 20,28) and 30 (25, 34) in SGA and AGA respectively, p = 0.06)]. HRV indices were reduced in the prone compared to supine position (p<0.0001), but reflex tilt responses were unchanged with position. SGA/AGA differences were independent of sleep position. GA weight status did not influence the likelihood of arousal, but prone sleeping per se reduced the odds 2.5-fold. The findings suggest reduced autonomic activity and cardiac reflexes in SGA infants. The finding that the sympathetic component of the control of HRV was higher in SGA infants could link with findings in adulthood of an association between being born SGA and a higher risk of cardiovascular disease.