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Background: Influenza is a contagious respiratory infectious disease out breaking in cold seasons of the year. The outbreak of the new influenza A (H1N1) virus in 2009 involved large populations of the world with considerable mortality. Hemagglutinin (HA) molecule, the main surface glycoprotein of the influenza virus, is one of the key factors for serological diagnostic kits and vaccine development. Thus establishment of HA gene bank of the circulating influenza viruses is essential in gaining quick access to large amounts of protein. Materials and Methods: The first step in providing such a bank is detection and isolation of HA full genome and its subunits by using specific primers and cloning them in proper vectors. For this purpose, using standard virus genome (A/New Caledonia/20/99(H1N1)) cultured on MDCK cell, HA coding gene was proliferated by RT-PCR using specific primers. Results: Isolation and cloning of the HA gene was verified by RT-PCR, enzyme digestion and determining nucleotide synonymy. Through the use of specific cloning primers, different HA gene constructs were propagated for expression of the gene in insect cells and E.coli bacteria. Conclusion: The results indicated the complete compatibility of the extracted HA gene with the influenza (A/New Caledonia/20/99(H1N1)) hemagglutinin. It makes it possible to use the gene as a source of cloning in a variety of eukaryotic and prokaryotic expression systems. [ABSTRACT FROM AUTHOR]