Abstract: Objective　To analyze the pathogen distribution and antibiotic susceptibility of deep sputum specimens from neonates with congenital esophageal atresia (CEA). Methods　The medical records of neonates with CEA hospitalized in the Children’s Hospital of Chongqing Medical University from Jan 2004 to Oct 2014 were reviewed, and the data of pathogen distribution and their antibiotic susceptibility were further analyzed. Results　One hundred and twelve bacteria were obtained by 104 cultures from sputum specimens in 55 patients. The most common 5 of Gram-negative bacilli were Pseudomonas aeruginosa (n=36), Klebsiella pneumoniae subspecies pneumoniae (n=29), Acinetobacter baumannii (n=19), Escherichia coli (n=9) and Maltophilia Aeromonas (n=6). Gram-positive cocci were only found in five cases (Hemolytic staphylococci in 2 cases, Viridans streptococcus in 2 cases, and Staphylococcus aureus in 1 case). Drug sensitivity analysis showed that the antibiotic susceptibility of these Gram-negative bacilli to semi-synthetic penicillin and cephalosporin were less than 50%, and more than 80% to carbapenems, aminoglycosides and quinolones. The sensitivity of Gram-positive cocci to vancomycin, teicoplanin Lalin was 100%. Conclusions　The pathogen of lung infection in neonates with CEA were mainly G- bacilli, which retained low susceptibility to most semi-synthetic penicillin and part of cephalosporin while remained highly sensitive to carbapenems, aminoglycosides, and quinolones. The Gram-positive cocci remain high susceptibility to vancomycin and teicoplanin Lalin.