BackgroundCow's milk protein allergy (CMPA) remains relatively understudied in Latin America.MethodsIn this observational study, we enrolled 64 patients with a median age of 3 months, of whom 60% were male. Patients included had a history of IgE‐mediated reactions with IgE sensitization or non‐IgE‐mediated reactions or symptoms following exposure to cow's milk. They underwent skin prick test, ImmunoCAP, fecal calprotectin (FC), and fecal eosinophil‐derived neurotoxin (EDN), in addition to double‐blinded placebo‐controlled oral food challenges (DBPCFC), with clinical evolution and tolerance acquisition observed over 1 year.ResultsMalnutrition was present in 78.1% of patients, and 87.5% had a family history of atopy, with 51.6% receiving exclusive breastfeeding. Gastrointestinal manifestations were prevalent in 90.6% of patients, followed by dermatological manifestations (10.9%), with only 2 experiencing anaphylaxis. IgE‐mediated CMPA was observed in only six patients. In those with non‐IgE‐mediated CMPA, FC had a median of 284 mg/dL (IQR: 138.5–415.5), while EDN had a median of 508.5 mg/dL (IQR: 160.25–868). One year after diagnosis, median FC significantly decreased (p < 0.0001), and malnutrition prevalence reduced to 17.1%. Moreover, 81% of patients acquired tolerance following DBPCFC, with 52% utilizing nutritional replacement formulas at diagnosis. Notably, 94% of those extensively hydrolyzed casein‐based formulas achieved tolerance (p = 0.08).ConclusionOur findings provide a foundational framework for future investigations into CMPA diagnosis, tolerance acquisition, and the utilization of hypoallergenic formulas tailored to the unique characteristics of our region.