Introduction: In order to prevent H5N1 virus infection from poultry to human, rapid virus detection, isolation and handling of the infected flock(s) play an important role. In this study, a mRT-PCR method was applied for rapidly detecting H5N1 virus circulated in poultry. Methods: The study was conducted on 53 clinical specimens collected from sick or dead poultry from avian influenza outbreaks occurred in northern Vietnam during the period from 2008 to 2009. Total RNA of each specimen was extracted then used as template for detecting H5N1 virus by the mRT-PCR method. Results: Fifty three clinical specimens collected from poultry were examined for detection of H5N1 RNA by the mRT-PCR and 29 specimens were found positive. The positive specimens were collected from 14 places in 7 provinces (or cities): Cao Bang, Ninh Binh, Lao Cai, Ha Noi, Son La, Dien Bien and Thai Nguyen. Conclusion: The mRT-PCR method can tie applied for diagnosis in suspicious H5N1 virus infections or large-scale screening of H5N1 virus in influenza epidemic surveillances in poultry.