This investigation evaluated variations in resting heart rate (HR) measures during the first half year of life in healthy, full-term infants who were either breast-fed (BF), or fed formula with (milk-based: MF; soy-based: SF) or without (soy-based: SF(-)) commercially supplemented DHA (decosahexaenoic acid). In infants fed the DHA-deficient diet, higher HR and lower values for heart rate variability measures were observed, indicating decreased parasympathetic tone in this group. These effects, appearing at 4 months and continuing for the remainder of the study period, are consistent with suggestions that the 3-5-month postnatal interval may be an important period in the development of cardiovascular regulation. The absence of these effects in SF infants receiving the DHA-supplemented formula suggests that neither soy protein nor the associated phytochemicals in soy formula contribute to these effects to any appreciable extent. In general, the results do not indicate differences in any of the study variables attributable to soy formula per se.