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Introduction: The first H5N1 outbreak in Burkina Faso was reported to the World Organization for Animal Health on 3 April 2006. This study aimed to determine the prevalence of avian influenza virus, infectious bronchitis virus, and Newcastle disease virus among domestic and wild birds in highly pathogenic avian influenza (HPAI) H5N1 outbreaks areas., Methodology: We collected paired tracheal and cloacal swabs from 283 birds including 278 domestic and five wild birds (three vultures, one sparrowhawk and one Western Grey Plantain-eater) in the Central Region (Ouagadougou) and the Western Region (Bobo-Dioulasso and Sokoroni) of Burkina Faso. Total RNA extracted from samples were subjected to reverse transcription  and resulting cDNA amplified by PCR using specific primers for detection of Avian Influenza Virus (AIV mainly highly pathogenic H5N1), Infectious Bronchitis Virus (IBV), and Newcastle Disease Virus (NDV) for the first time in Burkina Faso., Results and Conclusions: Our results show that 13.8% (39/283) samples were reactive for NDV, and the prevalence of IBV was 3.9% (11/283). None of the 283 birds were co-infected by AIV, IBV and/or NDV in our study areas. The prevalence of influenza A virus was 3.2% (95% CI: 0-6.6) with a 1.7% (95% CI: 0-3.2) prevalence of H5N1 being detected. Positive cases of H5N1 virus were found in two out of three vultures in Ouagadougou, and in three out of 203 local chickens in the Western Region. These results confirm the presence of influenza A H5N1 virus, IBV and NDV in domestic and wild birds in Burkina Faso.