Milk and formula-induced allergies may present with rash (atopic dermatitis/eczema), vomiting, wheezing, and/or cough.  Cow’s milk allergy is the usual cause. But studies show that 10-14% of infants with cow’s milk allergy also have cross reaction to soy (Of course. that also means that 86-90% will not have an allergy to soy. But there are also a few infants and children who do have traditional allergy and instead have what is called a non-IgE reaction to milk. Those children may have a 40% cross reactivity to soy (meaning again 60% of those few infants should tolerate soy). 

And thus, the majority of infants are likely to tolerate soy, allows most milk-intolerant infants to use soy formulas safely and with less expense than immediately employing an extensively hydrolyzed casein formula ($14 vs 25 per can, a difference of over $70/month for Nutramigen or Alimentum).  

This differs from other organizations' recommendations to use an extensively hydrolyzed casein formula. Those more expensive formulas can be used in those who do not wish to use soy. In the past, there has been concern about the phytoestrogens contained in soy husks; however, studies have shown that this weak estrogen has not made any difference in sexual development or fertility for adults who were originally raised on soy decades before.  

When there is a strong family history of allergy (marked by asthma, eczema, allergic rhinitis or food allergy in a brother, sister or parent), a European study (that did not include soy as an option) showed that elimination of cow’s milk with an extensively hydrolyzed formula used instead may lessen the eventual development of atopic dermatitis and childhood food allergies. As a result, your physician may wish to try an extensively hydrolyzed casein formula first or after a soy trial.

 For older infants and toddlers who would normally be on actual cow's milk (after they've transitioned from formula) but are unable to tolerate the milk. Soy "milk" remains the first choice because it has the most protein of all the alternative milks (see the table below). But if a toddler is unable to tolerate the soy or has an allergy to it, the other alternative milks can be tried, making sure the toddler has other good sources of dietary protein.

                                      Protein in 8 oz

                             Cow's milk                    8 grams

                             Soy                               5-7

                             Rice                               1-2

                            Almond                         1-2

 Adapted from An Evidence-Based, Cost-Sensitive Infant Formula Algorithm for the Infant on Georgia’s WIC Program. Stanley A Cohen and Kylia Crane RD, 2013