Heart rate variability (HRV), a measure of cardiac autonomic control, was analyzed in infants to assess the hypothesis that early undernutrition may induce autonomic dysfunction that could play a role in the programming of later cardiovascular disease. HRV data were collected during a night session in 546 healthy infants at 5–12 weeks of adjusted age, and statistical associations with fetal and postnatal growth indices were established. A significant positive correlation between birth weight, the ratio of neonatal weight to head circumference and postnatal weight gain, and HRV indices mostly influenced by sympathetic activity was demonstrated in 11- and 12-week-old infants. A slight correlation (p > 0.05) was also found in younger infants. These data suggest the influence of fetal and postnatal growth on the programming of the autonomic nervous system beyond the neonatal period. This influence may be one of the important mechanisms that link impaired growth in fetal and infant life to high blood pressure and other cardiovascular disease during childhood and adulthood (the Barker hypothesis).