Infectious bursal disease virus is an important poultry pathogen. It is distributed worldwide and causes significant economic losses. In this study, a system was adopted for the simultaneous monitoring of vaccine and virulent strains using reverse transcription polymerase chain reaction (RT-PCR). After the decay of maternal antibodies, chickens were vaccinated at the age of 37 days with a virus of intermediate virulence and challenged at 5, 10 and 14 days post vaccination (dpv). The challenge was done with IBDV strain CH/99. Sequencing of the hypervariable region of VP2 has shown that CH/99 belongs to the very virulent group of viruses. The vaccine virus could be found in the bursa of Fabricius, spleen, thymus and bone marrow until 24 dpv. The CH/99 challenge virus was found in the bursa and lymphoid organs when chickens were challenged at 5 and 10 dpv. When challenge was performed at 14 dpv, the pathogenic virus could not be found in the bursa and other lymphoid organs.