This paper investigates the trends of Impact Factors and self-citation rates of journals indexed in the JCR by two neighbouring countries Iran and Turkey for a period of five years (2000- 2005). All data extracted from the Journal Citation Reports – Science Edition (2000-2005). The study showed that the portion of Turkish journals entering data to the JCR data bank is two times higher than the portion of Iranian journals. From a total number of 6,088 journals in the JCR in 2005, 3 (0.05%) were published in Iran and the same number of journals published in Turkey. The 6,088 journals in the JCR produced 847,114 articles, 159 (0.02%) appeared in the Iranian journals and 352 (0.04%) in the Turkish journals. Of the 22,353,992 citations in 2005, 214 (0.001%) came from Iranian journals and 911 (0.004%) came from Turkish journals. The self-citation tendency by Iranian journals has increased dramatically throughout the period of study, it reached from 8% self-citation rate in 2000 to 18% in 2005, an increase of 2.25 times, whereas the self-citation rate by Turkish journals showed a negative trend, its self-citation rate fell from 22% in 2002 to 15% in 2005. The Impact Factors of Turkish journals showed faster growth than the Iranian journals, the mean value of Impact Factor for Turkish journals in 2000 was 0.49 under than the mean value of Impact Factor for Iranian journals, but in 2005 the mean value of Impact Factor for Turkish journals stayed 0.14 higher than the mean value of Impact Factor for Iranian journals.