Infectious bursal disease (IBD), commonly known as “Gumboro Disease is an infectious viral disease of chickens inducing severe immunosuppression. In Pakistan, imported vaccine is used to prevent the disease but there have been outbreaks even in vaccinated flocks. This indicates that there is variation among the locally prevalent viral strains and commercially available vaccine strain. In present study, twenty-five local strains of IBD virus (IBDV) were isolated, purified and their structural polypeptides were studied by polyacrylamide gel electrophoresis (PAGE). Then their protein profiles were compared with commercial vaccine D-78 strain. Distinct banding patterns were observed  in local isolates on basis of which the viral isolates were placed in three groups. Group-1 contained polypeptides of molecular weights 95Kd, 60Kd, 56Kd, 45Kd, 31Kd, 21Kd and 14Kd. In group-2, bands of 56Kd and 32Kd were missing whereas in group-3 the bands of 56Kd and 31Kd were missing while comparing with group-1. It was observed that 60Kd molecular weight protein band was common in all the three groups but it was absent in the vaccine D-78 strain. Vaccine D-78 strain appeared to have the banding pattern as 95Kd, 53Kd, 46Kd, 40Kd, 32Kd and 27Kd. Western blot analysis of the proteins were also conducted using antibodies raised against vaccine strain D-78. It was observed that the antibodies bind against all the protein bands of vaccine D-78 but did not bind with all the polypeptides of locally prevalent field viruses. This confirms that antigenic heterogenicity exists among the indigenous strains and the imported vaccine strains of IBDV.