Infant formulas based on whole soy protein isolates and supplemented with suitable vitamins and minerals to ensure they conform to relevant regulatory standards may be appropriate for use in healthy children. However, between 40% to 60% of infants with milk allergy are also allergic to soy milk.

In 1998 the American Academy of Pediatrics produced recommendations for the use of soy-based infant formulas; it was concluded that infants with documented gastrointestinal allergens are frequently sensitive to soy protein and should not be given isolated soy protein-based formula routinely.

The soy protein-based formula should not be recommended for any infant less than 6 months of age.
Recent concerns have also been raised regarding the high concentrations of phytoestrogenic isoflavones in soy-based formula: the daily exposure of infants to isoflavones in soy-infant formulas is 6-11 fold higher than the dose that has hormonal effects on adults consuming soy foods. It has been suggested that adverse biological effects including premature pubertal maturation and infertility may occur in infants fed soy-based formulas.
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