The parasympathetic nervous system (PS) influences are critical in the autonomic control of the heart. To examine how early postnatal diet affects PS development, we used a measure of tonic PS control of cardiac activity (vagal tone) derived from resting heart rate recordings in 158 breastfed (BF), 159 milk formula‐fed (MF) and 148 soy formula‐fed (SF) infants at ages 3, 6, 9, 12 and 24 mo. Artifact‐free recordings were analyzed using mixed models adjusted for gestation, SES, maternal IQ and scores on standardized measures of psychopathology. Across the study period vagal tone increased with age for all groups (p < .001) and was higher in SF than MF or BF infants (p ≤ .05), but the rate of increase slowed sooner for BF infants (BF at 6–9 mo; MF and SF at 9–12 mo) and vagal tone remained lower in BF infants after 9 mo. Thus, PS control of heart rate differs between BF and formula‐fed infants. The earlier slowing of vagal tone development in BF than formula‐fed infants has the effect of establishing a lower level of resting vagal tone in BF children. Since higher resting vagal tone has been associated with better neurodevelopmental and neurocognitive outcomes, these data suggest advantages for formula‐fed infants, particularly SF boys, compared with BF infants for these outcomes. Supported by USDA ARS CRIS 6251–51000‐006–03S