Microelements and vitamins are believed to have immunomodulatory effects. The aim of the study was to establish the role of antioxidants (vitamins A, E, D) and microelements such as copper (Cu), selenium (Se), and zinc (Zn) levels in allergic diseases in schoolchildren. The study uses a cohort of 80 children (40 with and 40 without allergy/asthma diagnosis) aged 9 to 12 years recruited for the Polish Mother and Child Cohort Study. At nine to twelve years old, the children were tested for microelement and vitamin content and health status (including skin-prick test and spirometry, urine cotinine level). Demographic data were collected from mothers by an allergist. The risk of asthma occurrence was found to be significantly related to the levels of Cu and Zn. The level of Cu was also particularly closely associated with allergic rhinitis and was indicated as a significant predictor of food allergy. The levels of Cu and Zn, and poor nutritional status in general, can influence the immune system and may be considered risk factors for developing asthma, allergic rhinitis and food allergy.