The objective of this study was to compare the effect of two conventional H9N2 avian influenza (AI) vaccines on replication and shedding of the H9N2 AI virus in broiler chickens. These inactivated oil emulsion vaccines contain either a UAE or an Iranian H9N2 AI isolate. One hundred and fifty one-day-old commercial broiler chickens were randomly divided into six groups. The birds, except for the control group (group 4), were challenged with a low pathogenic A/Chicken/Iran/SH-110/99 (H9N2) virus isolate. Birds in groups 1 and 5 were vaccinated with an Iranian AI vaccine and groups 2 and 6 with an UAE vaccine type. Birds in groups 5 and 6 were also vaccinated with an H120 strain of infectious bronchitis live vaccine. On days 3, 7, 11, and 15 post inoculations (PI) the trachea, lungs, kidneys and faeces were collected for molecular detection and quantitation of the H9N2 AI virus using TaqMan real time PCR assay. The results showed that frequency of virus recovery and viral titration was generally higher for unvaccinated challenged birds (group 3) on all days PI. No virus was detected in the chicks of group 1. The virus was detected in some cases in the tracheas and lungs of chicks in groups 2, 5 and 6. However, there was no statistically significant difference in viral replication in the trachea and lungs between chicks vaccinated with the UAE and Iranian type vaccines. The most frequent detection of the virus was in the kidneys in comparison with the other samples. The viral titer in the kidneys of unvaccinated challenged birds (group 3) on day 3, 7, 11 and 15 PI was higher than those of the same organs in the vaccinated challenged birds (groups 1, 2). The highest titer of the virus was observed in the faeces of unvaccinated challenged and the chicks vaccinated with the IB and UAE type vaccine (group 6) on day 7 PI. There was a statistically significant difference in viral shedding between groups (1 and 3), (2 and 3) and (5 and 6) (P=0.008). Infectious bronchitis live vaccine could increase the AI virus propagation and shedding in co-infected groups (groups 5 and 6). Altogether, both AI H9N2 vaccines could effectively reduce viral replication and shedding in broiler chicken, however, in order to achieve efficient control of the disease, vaccination should be accompanied with other preventive measurements including biosecurity practices.