Objective: To evaluate the dietary intake and the anthropometric profile of infants on a diet eliminating cow’s milk proteins (CMP), compared to infants on a free diet. Method: Prospective cross-sectional study carried out with infants aged 6-24 months, in the gastroenterology and childcare/pediatric outpatient clinics of a children’s hospital. The anthropometric evaluation included weight, height, head and arm circumferences, tricipital and subscapular skinfolds, ranked by z-score according to the World Health Organization. Dietary intake was assessed by two 24-hour food recalls, expressed in energy, carbohydrates, proteins, lipids, vitamins and minerals and was compared with the dietary reference intakes (DRIs). Results: 43 infants on a CMP-elimination diet and 47 infants on a free diet (12.66 ± 4.97 months) were evaluated. When compared to the group on a free diet, the group on an elimination diet showed shorter height (p=0.026) and lower intake of vitamins B1 (p=0.020), B2 (p=0.000), B5 (p=0.007), B12 (p=0.025), D (p=0.006), except for vitamin K (p=0.009), and minerals calcium (p=0.000), phosphorus (p=0.000) and zinc (p=0.030). The intake of most nutrients with significant differences was in accordance with or greater than the recommendations of the DRIs in the exclusion diet group, with the exception of calcium and vitamin D, which was lower in at least one of the daily intake recommendations. Conclusions: Infants on a CMP-elimination diet were shorter and showed lower intake of some vitamins and minerals compared to the group on a free diet, although within the normal range according to the DRIs, except for calcium and vitamin D.