Adverse reactions to cow’s milk proteins are usually indicated as cow’s milk allergy/intolerance (CMPA/CMPI) because no differentiation is possible on the basis of symptoms, and there is no reliable single laboratory test available for the diagnosis of CMPA or CMPI. Elimination and challenge tests for cow’s milk proteins using strict, well-defined diagnostic criteria are required for the diagnosis of CMPA/CMPI. Atopic dermatitis (AD) is one of the most common symptoms of CMPA/CMPI. Approximately one third of AD children have a diagnosis of CMPA/CMPI according to elimination diet and challenge tests, and about 40–50% of children <1 year of age with CMPA/CMPI have AD. Many children with AD and CMPA/CMPI develop a complete tolerance to CMP in a few years. Children with persisting forms of CMPA/CMPI have a more frequent history of familial atopic disease, change in CMPA/CMPI manifestations over time and very high frequency of multiple food intolerance and allergic diseases. Many children who outgrow their AD develop other allergic diseases, such as rhinitis or asthma. The simultaneous development of allergic tolerance in one organ and the intolerance or atopic disease in another organ suggest that genetic, immunologic and environmental factors play a complex role in the natural history of AD and other atopic diseases.