Observational studies have shown that allergic infants, irrespective of the type of diet, show various degrees of growth depression in the first year of life. We investigated whether the type of milk in the complementary feeding period (6–12 months of age) is associated with differences in the increase of standardized growth indices (weight-for-age, WA; length-for-age, LA; and weight-for-length, WL, z-scores) in infants with cow's milk allergy (CMA). Infants with immunoglobulin E-mediated CMA breastfed at least 4 months and progressively weaned in the 5- to 6-month period were randomly assigned to three special formulas, a soy formula (n = 32), a casein hydrolysate (n = 31), and a rice hydrolysate (n = 30). A fourth, non-randomized group was made up by allergic infants still breastfed up to 12 months (n = 32). Groups were compared for WA, LA, and WL z-scores at 6, 9 and 12 months of age. All groups showed low WA and LA z-scores at 6 months of age. Infants fed hydrolyzed products showed a trend toward higher WA z-score increments in the 6- to 12-month period. The use of casein- and rice-based hydrolyzed formulas resulted in higher changes in WA compared with soy formula. Further research should be aimed at optimizing the dietary needs and feeding regimens for infants with CMA.