ObjectiveTo investigate the distribution and drug resistance of pathogens in neonates with lower respiratory tract infection, and provide evidence for clinical rational antibiotic use. MethodsA retrospective analysis on 998 strains isolated from 5 486 sputum samples during January 1, 2009 to December 31, 2012 collected from hospitalized neonates was performed. ResultsOf the 998 isolated strains, the common pathogens were Klebsiella pneumoniae (23.1%), Escherichia coli (E. coli) (21.2%), Staphylococcus aureus (19.4%), and Enterobacter cloacae (8.4%). Klebsiella pneumonia, E. coli and Enterobacter cloacae were generally resistant to penicillin, but enzyme inhibitors could reduce the resistance rate. A large proportion of Klebsiella pneumonia was resistant to the third generation cephalosporins (78.4%), while E. coli and Enterobacter cloacae had a lower resistance rate (46.7% and 46.5%, respectively). There were 7 strains (3.0%) of Klebsiella pneumoniae and 1 (1.2%) strain of Enterobacter cloacae resistant to imipenem. Twenty-three strains (13.6%) of Klebsiella pneumoniae, 1 strain (0.7%) of E.coli and 1 strain (2.5%) of Enterobacter cloacae were resistant to ertapenem. A total of 97.0% of Staphylococcus aureus was resistant to penicillin, but only 11.0% was resistant to oxacillin, and all the isolates were sensitive to vancomycin. ConclusionGram negative bacteria are the common pathogens in the hospitalized neonates in our hospital. Klebsiella pneumonia, E. coli and Staphylococcus aureus are the common pathogens. The common pathogens show a high resistant level to antibiotics. Clinicians should evaluate the potential pathogens of infections based on the results presented in our study, in order to select antibiotics rationally when treating infections.