Objective:To analyze the nucleic acid detection result of suspected HFMD patients in Sanmen,and provide scientific basis for prevention and control of hand,foot and mouth disease.Methods:45 throat swabs and herpes fluid samples were selected from 34 HFMD patients during April to September in 2010.After extraction of viral RNA,one step RT-PCR was used to detect genes in Vp3-Vp1 region of EV71 and genes in Vp3~Vp1 region of Cox-A16,then the positive rates of the two were compared.Results: 43 samples were found total intestinal virus nucleic acid positive from 45 specimens,in which 26 samples were CoxA16 nucleic acid positive,11 samples were EV71 nucleic acid positive and 6 samples were positive for both CoxA16 nucleic acid and EV 71 nucleic acid.Conclusion: The positive rate of total intestinal virus nucleic acid in HFMD nucleic acid detection was high with the CoxA16 and EV 71 as dominant.RT-PCR detection has important value for early diagnosis and infectivity judgement of HFMD.