Abstract: Objective To observe the effect of automatic nucleic acid detection analysis system in detection of hepatitis B virus(HBV), hepatitis C virus(HCV)and human immunodeficiency virus(HIV)in blood samples of blood donors. Methods A total of 1 229 volunteer blood donors were selected, two copies of blood in each donor were collected, 1 copy was used for Enzyme Linked Immunosorbent Assay(ELISA)and another one was used for nucleic acid detection. Results The positive ratesof HBV by nucleic acid test and ELISA test were 2.03% and 0.98%, respectively, there was significant difference(P<0.05). The positive rates of nucleic acid test and ELISA in detecting HCV were 1.22%and 1.14%, there was no significant difference(P>0.05). The positive rates of nucleic acid test and ELISA in HIV detection were 0.24%and 1.06%, there was significant difference(P<0.05). Conclusion Automatic nucleic acid detection analysis system has higher accuracy rate in screening HBV, HCV and HIV in voluntary blood donors, nucleic acid detection and ELISA detection have their own advantages, and the combination of the two methods can improve the accuracy of virus detection.