We present here a new allergenicity prediction method. The method uses information about spatial structures of proteins. Prediction of protein allergenicity was based on search for similarity between linear fragments from a sequence of a query protein and peptides (linear and discontinuous) from known allergens. A sequence of query protein was subdivided into linear fragments of 8 amino acid residues applying a sliding window. Similarity between fragments and peptides was calculated taking into account physical-chemical properties of amino acids.