Cow’s milk protein allergy (CMPA) in Latin America is little studied. We conducted a prospective study in 64 patients with a median age of 3 months, 39/64 (60.94%) were male, 23/64 (35.93%) had malnutrition, 56/64 (87.5%) had familiar atopy, 34/64 (51.56%) were receiving exclusive breastfeeding (EBF). The patients passed a medical evaluation by the specialist and underwent: Prick Test, ImmunoCAP, Fecal Calprotectin (FC) and fecal eosinophil derived neurotoxin (EDN), double-blind placebo control oral food challenges (DBPCFC) and were observed for one year regarding their clinical evolution and acquisition of tolerance. 58/64 (90.63%) had gastrointestinal manifestations, 7/64 (10.94%) had a dermatological manifestation, 2/64 (3.1%) had respiratory manifestations and 2/64 (3.1%) had anaphylaxis. 6/64 (9.38%) had an IgE - mediated CMPA. In patients with Non - IgE Mediated CMPA, fecal calprotectin was found to have a median of 284 mg/dL and an interquartile range (IQR) of 138.5 - 415.5. EDN had a median of 508.5 mg/dL with an IQR of 160.25 - 868. One year after diagnosis, the median FC decreased significantly with p < 0.0001. Malnutrition after one year was reduced to 17.18%. Likewise, 52/64 (81%) acquired tolerance after practicing DBPCFC on them. 33/64 (52%) used nutritional replacement formulas from the time of diagnosis, those who used Nutramigen LGG 15/16 (94%) acquired tolerance after practicing DBPCFC while 12/17 (71%) of those who used other formulas acquired tolerance (p. 0.08). Our findings are a good starting point for future studies that explore the diagnosis, acquisition of CMPA tolerance, and the use of hypoallergenic formulas with the particularities of our region.