Objective To perform a bibliometric analysis of papers published by Second Military Medical University in journals covered by Science Citation Index (expanded) (SCIE) during 1994-2009, so as to provide evidence for decision making in scientific research adminstration. Methods The papers published in journals covered by SCIE authored by researchers of Second Military Medical University in 1994-2009 were retrieved and analyzed; the impact factor(IF) of 2008 published by Institute for Scientific Information（ISI）was used in the present study. Results A total of 3,539 papers were retrieved from 926 journals. Original article accounted for 83% of the total; those with an IF lower than 5 accounted for 77% and those with an IF higher than 10 accounted for 3.3%. There were 206 papers which had been cited for more than 20 times; the most active subject was immunology; and the closest cooperation in publication was with Shanghai Jiaotong University. Conclusion This study introduces the publication of scientific papers published by Second Military Medical University and their citations from a bibliometric perspective, which provides a quantitative reference for the scientific administration department and the researchers.