Objectives: Infectious bursal disease is a highly contagious, immunosuppressive disease of chickens. The bi-segmented double-stranded RNA virus is prone to some alterations in genome of virus. The objective of the present study was to characterize Iranian isolates of infectious bursal disease using RT-PCR of VP1 gene and compare these results with RTPCR/ RFLP patterns of VP2 gene in our previous study. Materials & Methods: Twenty-six Iranian IBDV isolates were characterized using RT-PCR of VP1 gene. Three IBDV isolates were sequenced and compared with published sequences of VP1 gene of IBDV strains around the world. Results & Conclusion: Molecular characterization of six isolates using amplified fragment of VP1 and VP2 was not the same. This discrepancy between results may be linked to genetic re-assortment of field isolates. The nucleotide and amino acid sequences of Iranian IBDVs were more closely related to a European stain (Holland), south-east Asian isolates origin, and a Turkish strain (OA/G1). There were 23 differences in nucleotide alignment of very virulent (except for IL and PT) and non-very virulent viruses. Amino acid alignment of strains showed that in two positions vvIBDVs (except for IL and PT) differ from classical and variant viruses. These residues may be potential markers of virulence in vvIBDVs. This is the first report of natural re-assortants between vvIBDVs and other IBDVs strains in Iran.

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