Highly pathogenic avian influenza (HPAI) is a viral disease caused by some H5 and H7 subtypes of influenza virus type A in most species of birds, especially poultry. HPAI viruses are amongst the most challenging viruses that threaten both human and animal health. Consequently, various strategies such as the use of vaccines have been proposed to control the disease. After a catastrophic pandemic and the failure of conventional methods (elimination and extermination) in Iran, multiple vaccines has been used to control the disease. This study investigates the immunogenicity of two recombinant inactivated commercial vaccines of H5N1 and H5N3 subtypes in laying pullet flocks in Tehran Province, Iran. From 32 halls in 6 breeding units of laying pullets, 3200 sera and 800 tracheal and cloacal swabs were collected. After collecting the samples, Serum neutralisation (SN) and hemagglutination inhibition (HI) tests were conducted on sera to determine the serum titers of H5 specific antibody obtained from vaccine inoculation in three steps: before, after first vaccination and after the second vaccination (booster). SN and HI tests were carried out by the alpha and beta methods on the pooled samples by the vaccine type (as antigen for HI and SN), and the results were compared. The PCR was performed on the tracheal and cloacal swab samples to possibly detect the HA (H5)virus in the studied flocks. The HI test results showed that both vaccines had a Serum antibody titre above 5 (log2) after two vaccination rounds, indicating a desirable immunogenic response. The SN test results also showed a neutralisation index above 104.5 for both vaccines, indicating more than 50% reduction in antigenicity of the virus. The PCR results were negative. This study was the first investigation of immunogenicity following two-time vaccination against H5 subtype vaccines in Iranian poultry flocks, indicated suitable antibody titer against the influenza virus in vaccinated flocks.