Objective To study the distribution and drugresistance of pathogens isolated from patients who suffered from lower respiratory infections after thoracotomy and provide basis for rational use of antibiotics in clinical practice. Methods A total of 118 patients suffered from lower respiratory infections after thoracotomy in Beijing Lung Cancer Center and the Thoracic Surgery Department of Xuanwu Hospital between January 1,2006 and December 31, 2009. We performed a retrospective study on pathogens from their lower respiratory tract. Of these patients, 89 are male and 29 are female with a mean age of 64.6 years. Sputum specimens were obtained by sterile sputum collectors or bronchofibroscopes, and then were sent to microorganism laboratory immediately. Cytological screening was carried out before specimen inoculation. Bacterial culture, identification and drug sensitivity test were performed with routine methods. Results A total of 201 strains of pathogens from the lower respiratory tract were identified. There were 126(62.7%) strains of gramnegative bacilli, 66(32.8%) strains of grampositive cocci, and 9(4.5%) strains fungi. The four prevalent gramnegative bacilli strains with the highest isolating rate between 2006 and 2009 included 34(27.0%) strains of acinetobacters, 28(22.2%) strains of verdigris Pseudomonas, 19(15.1%) strains of Klebsiellas and 19(15.1%) strains of Escherichia coli. Verdigris Pseudomonas ranked first in isolating rate among prevalent gramnegative bacilli strains from 2006 to 2008, but it was replaced by cinetobacters (9 strains, 40.9%) in 2009. The most prevalent strains of grampositive cocci were staphylococcus aureus (35 strains, 53%) from 2006 to 2009. Gramnegative bacilli were most sensitive to imipenem and no grampositive cocci were resistant to vancomycin. Conclusion Gramnegative bacilli are the most common pathogens in lower respiratory infections after thoracotomy and show extremely high drugresistance rate. Drugresistance monitoring of pathogens should be promoted. It may contribute to rational antimicrobial therapy and effective control of infections.