In the 90's of the XX century, 2 new and important allergens of house dust mites mites were cloned and sequenced: Mag 1 and Mag 3. However, the second allergen has been identified to date only in extracts of Dermatophagoides farinae [DF]. In this work, we aimed to detect expression of this important allergen and for the first time analyze to the amino acid sequence in other species of house dust mite - Dermatophagoides pteronyssinus [DP]. We were able to confirm the expression of allergen Mag 3 in DF and to exclude it in DP . By sequencing the products of DNA amplification, we revealed the nucleotide sequence encoding allergen Mag 3 in DF . This analysis enabled detection of 9 single base changes. An analysis of encoded amino acid sequence by triplets with substituted nucleotides revealed that 8 changes were polymorphic, and 1 was a mutation substituting GTG (valine) for ATG (methionine) at 236 position. However, the presence of amino acid sequence difference in this allergen might suggest that there exist other isoforms which can make difficult both diagnosis as well as immunotherapy in persons who produce allergic response to this allergen. The variants of allergen Mag 3 (group 14) are still not known beside the very good known allergen variants of the other main groups 1, 2, 4, 5 or 7. Thus, the identification and definition of allergic properties of allergen Mag 3 variants needs to be further investigated.