Background Cow's milk protein allergy (CMPA) is usually transient, with most children tolerating ingested cow's milk by 3 years of age. This study aimed to determine factors that promote or hindering the development of tolerance to CMPA. Methods A logistic regression model was used to determine independent risk factors associated with tolerance and persistence of CMPA. Result A total of 178 children diagnosed with CMPA were included in the study. The patients' median age was 32 months (minimum-maximum, 14 to 144 months), and their median follow-up period was 30 months (minimum-maximum, 12 to 54 months). In the follow-up, CMPA persisted in 62 (34.8%) patients. The patients were divided into 2 groups according to patient's age. Group I was <3 years old and group II was >= 3 years old. The factors independently associated with the persistence of CMPA for group I were as follows: comorbid food allergies (p = 0.021), the presence of an immunoglobulin E (IgE)-mediated reaction (p = 0.001), and respiratory system symptoms (ie, tachypnea) (p = 0.036). The presence of gastrointestinal-related discomfort (p = 0.001) was an independent risk factor associated with the development of tolerance. The presence of comorbid food allergies (p = 0.03) was the only independent predictive factor for CMPA persistence for group II. Conclusion The prognosis in cases of CMPA, a food allergy, is good, with tolerance developing over time. The presence of IgE-mediated CMPA, respiratory-related symptoms (ie, tachypnea), and the presence of comorbid food allergies have negative effects on tolerance.