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Background and Aim: Citation is one of the journals ranking factors. Self-Citation rates regarding journals `performance, especially in international databases, is important. The aim of this study is to examine the effect of Journal self-Citation on Impact Factor of Iranian English medical journals indexed in the Web of Science and Islamic World Science Citation Center.

Materials and Methods: The Impact Factor of 12 journals in WoS and 26 in ISC were studied during years 2006-2009 using citation analysis and Journal self-Citation. Self-Citation rate were calculated using cited journals and citing journals tables in ISC. Wilcoxon test and Mann-whiteny test were used for comparison of self-citation rate between two databases. In order to determine any correlation between journal self-citation and IF in WoS, Pearson test was used. In ISC, Spearman test was performed. For comparison of two correlations test, Covariance test was used.

Results: No significant difference between Journal self-citation rates in two databases was noted(p>0.05).There was a significant correlation between Journal self-citation and Impact Factor in WoS(p=0.007, r=0.64). The correlation was not statistically significant in ISC(p>0.05, rsp =0.23). There was not any significant difference between the relations of Journal self-citation and impact factor in two databases(p=0.526).

Conclusion: Attention to the Journal self-citation rates for comparison of Journal Impact Factor in WoS is more important than attention to the comparison of these journals between two Databases.