Abstract: The pathogens were tested in 682 cases of neonatal pneumonia,atypical pathogens were found in 167 cases (24.49%).Among the 167 cases,chlamydia trachomatis was detected in 124(74.25%),ureaplasma urealyticum in 55 (32.93%),chlamydia pneumoniae in 47 (28.14%) and mycoplasma pneumoniae in 35 (20.56%).The Chlamydia trachomatis-positive rate in mothers of 167 cases was 80.84%,ureaplasma urealyticum was 53.29%,chlamydia pneumoniae was 50.90%,Mycoplasma pneumoniae was 53.29%.The patients were treated with azithromycin and other antibiotics,151 cases were cured and 11 were effective with an overall efficacy rate of 97.01%.The liver and kidney function were tested before and after treatment; and there were no significant changes after treatment.The results show that azithromycin is safe and effective for treatment of neonatal infectious pneumonia from atypical pathogens.