Background: Food allergy which usually develops in the first year of life is a risk factor for persistent asthma in young children. Cow’s milk has been demonstrated to be the most commonly identified food allergen in children. Considering the central role of non-IgE-mediated food allergies in the development of hidden gastro esophageal reflux and consequently asthma, we evaluated the effect of eliminating food allergens to better control asthma. Method: A total of eighty infants and children up to the age of 12 referred to the Asthma Clinic of Mofid Children Hospital for a period of one year were enrolled in this study. In those patients whose asthma remained uncontrolled (Childhood Asthma Control Test ≤19) despite a 2-week period of treatment, we advocated a 2-week diet based on eliminating cow’s milk in conjunction with asthma conventional therapy. For breast-fed infants, moth ers were requested to eliminate these products from their daily intake regimens and for formula-fed infants, the elemental based formula was started. Results: Three of the patients were lost in follow-up and six of them were excluded from the study because of non-compliance. The Asthma Control Test score which was less than or equal to 19 in the entire study population, increased to 20 or more after we began a diet based on the elimination of cow’s milk in all but 13 participants. Conclusion: To conclude, the results were promising, demonstrating that a cow’s milk protein elimination diet is a prudent approach in the management of patients with recalcitrant asthma, and can be considered as the missing link in asthma treatment.