Objective To explore the clinical application of FP-PCR method to detect MP-DNA.Methods Five hundred and sixty-three children suspected of MP infection were enrolled in experimental group. FP-PCR was adopted to detect MP-DNA. MP-DNA was re-detected later in 60 children. At the same time,MP-Ab (MP antibody) was detected by means of particle agglutination. MP-Ab was re-detected one or two weeks later. Also 20 healthy children were selected as the control group. Results The positive rate of MP-DNA and MP-Ab were 34. 99% and 35.52% respectively,which showed no significant difference (x2 =0. 31, P > 0. 05). The coincidence of the two methods was 97. 69%. But the positive rate of MP-DNA was significantly higher than that of MP-Ab in the early stage(30. 48% vs 10. 16%) (x2 = 74. 46, P < 0. 05).The sensitivity and specificity of FP-PCR were 96. 00% and 98.62% respectively. The result of reviewed MP-DNA was consistent with the clinical diagnosis. Conclusion FP-PCR method is very sensitive, convenient and stable. It is fit for the clinical application ,especially the diagnosis of early MP infection. It helps to identify those who had been infected with MP before.