We investigated the self-citation rates of 884 Chinese biomedical journals, including 185 general medicine journals, 96 preventive medicine journals, 103 Chinese traditional medicine journals, 66 basic medicine journals, 370 clinical medicine journals, and 64 pharmaceutical journals. The average self-citation rates of these journals for the years 2005–2007 were 0.113 ± 0.124, 0.099 ± 0.098 and 0.092 ± 0.089, respectively, i.e. a downward trend year by year. The upper limits of normal values of self-citation rates for the same period were 0.316, 0.260 and 0.238, respectively. A significant difference was found in self-citation rate between biomedical journals of different subjects. 52 Chinese biomedical journals had no self-citation in 2007. The total citation frequency and impact factor of these 52 biomedical journals were 263 and 0.206, respectively, which were very much lower than the average levels of all Chinese biomedical journals in 2007. A self-citation rate higher than the upper limit was considered as excessive self-citation: 62 (7.01%), 68 (7.69%) and 66 (7.47%) biomedical journals showed excessive self-citation in the years 2005–2007, respectively. However, a certain amount of self-citation is reasonable and necessary.