The prevalence of food allergy and food intolerance is increasing and it is an important public health problem affecting children. Food allergy results from an immunological reaction to certain food(s) and affects numerous organs in the body. Food intolerances are non-immunological reactions including metabolic, toxic, pharmacological and undefined mechanisms. Cow milk is the most common cause of food allergy and food intolerance, especially in young children. Food intolerance can present with similar symptoms to those of food allergy. Health-care personnel, patients and their caregivers often confuse food intolerance with food allergy. This review focuses on the clinical manifestations, diagnostic evaluation, treatment and prevention of food allergy and food intolerance.