Objective To analyze the inherent quality of non-cited papers published in Chinese Journal of Endemiology, so as to identify the direction of invitation for contributions, and to provide the evidence for improving the academic quality and the cited rates. Methods Scientific papers published in Chinese Journal of Endemiology from 2004 to 2006, with zero cited rates were retrieved in China National Knowledge Infrastructure by March 24, 2011. These articles were statistically analyzed according to publication year, section type, download frequency, etc. Results A total of 200 papers were not cited, accounting for 23.04% (200/868) of the total number of papers published in the journal in the three years. Respectively, 17.23% (46/267), 24.39% (70/287)and 26.75% (84/314) of the papers published in 2004, 2005 and 2006 did not receive a single citation. The number of non-cited papers in editorial and expert forum column was zero, all articles in those column had been cited;followed by review column, non-cited rate was 6.98% (3/43);articles published in the column of short reports were seldom cited and non-cited rate was the highest of 54.02%( 121/224);all the columns of experimental study, field epidemiological investigation, clinical medicine, detection method and sanitary control had a certain percentage of non-cited papers. All of the 200 non-cited papers were downloaded, the download frequency ranged from 1 to 109, with an average of 27.21 times. Conclusions Adequate space should be given to the columns of editorial, expert forums, review, experimental study and field epidemiological investigation;the number of short reports should be reduced appropriately. The journal should enhance cited rate of published papers, comprehensively improve the academic quality of the articles, and contribute to the academic exchange and discipline development.