Abstract: Objective To develop a new method for fluorescent labeling technique, universal primer U2 labeling (UPL), for microarray studies.Method Influenza virus RNA was labeled with four labeling methods, namely UPL, random primer, restriction display incorporation labeling method and reverse transcription coupled random primer spiking labeling method (RT-PSL), respectively, and hybridized to influenza virus oligonucleotide microarray. The signals extracted from the microarrays were analyzed with SPSS 10.0 software to compare the efficiency and reproducibility of the labeling methods.Results The fluorescence intensity, signal-to-noise ratio (SNR), true positive ratio (TPR) of the probes and reproducibility of labeling with UPL were comparable with those RD-labeling method, and higher than those of RT-PSL method. UPL reduced the complexity of the procedures in comparison with the other labeling methods.Conclusion UPL labeling method can be used in research and development of the microarray technique.