Objective To investigate the respiratory tract infection of suffering children by 9 atypical pathogens in Haikou region,and definite the distribution of atypical pathogen. Methods Based on indirect immunofluorescence assay,blood IgM levels had been simultaneously detected of 9 atypical pathogens,which isolated from＜1 year old,1~2 years old,2~3 years old,≥3 years old children with respiratory tract infection from July 2011 to June 2012.And then the positive cases had been epidemiological clinical analysed. Results The total positive rate of atypical pathogen was 34.69%(417/1 202),the mixed infection positive rate was 4.58%(55/1 202),all most the mixed infection cases were infected by MP and other 1 or 2 pathogens together.The positive rates 31.53%,5.41%,1.16% of MP,INFB,RSV respectively were the frist,second,third highest rate,the cases infected by COX or CP were the least in 9 atypical pathogens.In April (March of lunar calendar),the total positive rate was 47.57%,it was the highest,and the total positive rate of winter and spring was higher than that of summer and autumn.The total positive rate increased as the age increased.In ＜1 year old group,the positive rate of MP was the highest,and the second highest was the RSV's,but in the other group,the first and the second highest positive rate were MP's and INFB's.The positive rate of MP in female was higher than that in male. Conclusion The distribution,the peak onset season and the positive rates of 9 atypical pathogens in respiratory tract infection children in Haikou are different to the other region.