ObjectiveTo compare effect of enterovirus (EV) 71 nucleic acid detection and EV71-IgM antibody detection on clinically diagnosis of hand-foot-mouth disease in children. MethodsRectal swabs collected from 1379 children who were clinically diagnosed from April 20, 2011 to September 10, 2011 as suspected patients with the handfoot- mouth disease were detected by fluorogenic quantitative polymerase chain reaction to conduct EV71 nucleic acid detection. Meantime, enzyme-linked immunosorbent assay was used to conduct EV71-IgM antibody detection in serum samples collected from those children. ResultsIn these 1379 cases, 79 had positive EV71 nucleic acids with a positive rate of 5.73%; while 82 cases had positive EV71-IgM antibodies with a positive rate of 5.95%. There were 32 cases with positive EV71 nucleic acid and positive EV71-IgM antibody. The rate of consistent results of two detection methods was 95.2%. The positive rates of two methods had no negligible differences (χ2=0.093, P=0.761). ConclusionCombination of EV71 nucleic acid detection and EV71-IgM antibody detection, can improve the efficiency in diagnosing hand-foot-mouth disease in children and facilitate the protection and diagnosis of the disease.