Researchers from the Claude Bernard University in France found that babies who are breast-fed have lower blood pressure when they are three years old compared with babies who are given formula with high amounts of protein.
In addition, breast-fed babies were also found to have slightly bigger heads than those who were fed a low-protein formula.
However, according to the researchers, the level of blood pressure and head circumference of the children in the study were within normal range, regardless of the food they ate, LiveScience reported.
Breast milk is considered the best source of nutrition for babies, although it is low in vitamin D. While some women choose not to breast-feed, some cannot because of biological problems or some other issues.
For the study, which was presented at the Paediatric Academic Societies in Denver, the researchers looked at 234 infants who were divided into three groups.
One group was exclusively breast-fed for the first four months, while infants in the other two groups were given either a low-protein formula, or a high-protein formula. The protein content in both formulas is within the recommended levels for children this age, the researchers said.
All infants were enrolled in the study before they were a week old. When the infants were 15 days old, those who were breast-fed had lower levels of the hormone insulin in their blood compared with babies who were given formula.
However, this difference disappeared by the time the babies were nine months old.
Although there was no difference in their body length, weight or composition of fat when the kids were three years old, those who were fed the low-protein formula had head circumferences that were on average, 0.2 inches smaller than those who were breast-fed.
Breast-fed babies also had a lower average blood pressure reading compared to those who were fed the high-protein formula (69.72 mmHg vs. 74.05 mmHg.)
"It appears that formula feeding induces differences in some hormonal profiles as well as in patterns of growth compared with breastfeeding," study researcher Dr Guy Putet said in a statement.
"The long-term consequences of such changes are not well understood in humans and may play a role in later health."
The researchers think the amount of protein in the babies` diet may play a key role in prompting these differences.
If babies cannot be breast-fed, they should be given formulas that produce a growth and hormone pattern similar to that of breast-fed infants, Putet said.