【Objective】 To recognize the clinical epidemiological characteristics of acute lower respiratory infection (ALRI) children patients infected by three kinds of atypical pathogens through investigated it between the year 2003 and 2007 in Kunming region. 【Methods】 Based on indirect immunofluorescence assay, simultaneously detected blood IgM levels of M-pneumoniae (MP), L-pneumoniae(LP1) and Chlamydia pneumoniae (CPn) from 12 083 hospitalized children patients between 2003 and 2007, so that acquired statistics results through investigations of the age and gender distribution characteristics, of atypical pathogen infection and of the epidemiological features of the five years' results. 【Results】 The combined infection rate by atypical pathogen in Kunming region between the year 2003 and 2007 was 30.1%; the infection rate by Mp, LP1 and CPn were 17.3%,11.3% and 1.4%, respectively. In autumn and winter the infection rates were the highest. In the summer and autumn of 2003 and in the autumn and winter of 2007, there seemed Mp outbreaks in the local area. The infection rates by Lp1 in summer and autumn were higher than those in spring and winter. Children infected by CPn showed the epidemiological characteristics or sporadic infection all year round. Atypical pathogen infection rate increased as the children grew up. Mycoplasma pneumoniae was the main local causative agent responsible for ALRI children aged above one yers's old in Kunming region. 【Conclusions】 MP and Lp1 are the two leading atypical pathogen lnfection of children in Kunming region. Infection rate varied from seasons. The atypical pathogen infection rate increases with children grow up.