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Background and Aim: The production of science is the key element of program to achieve sustainable development. Currently, the most important characteristic to produce knowledge is the number of document indexed from scientific journals in databases that do bibliometry and Scientometrics study. The aim of this study is evaluation of scientific production of Iranian medical domain based on the document indexed form scientific journal in chosen database, between 2005-2009.

Materials and Methods: Analytical- descriptive method and bibliometry analytic was adapted. The study population includes all scientific journals that was published in English and indexed in WOS and Scopus until of the time of this study. Data collection tool was check list that was made by researchers & complete by referring and direct observation in WOS and Scopus databases. Data was analyzed by SPSS and other statistical methods.

Results: Showed that from 44 journals title that studied, 18 titles was indexed in WOS and 20 titles was indexed in Scopus. The number of records and citation, according to the review with passing year, has been rising. Maximum number of documents and citations are related to the final years. Number of records in the Scopus database is more than WOS, but the differences in not significant (P- value = 0/186).

Discussion and Concoction: Journals visibility in the medical science filed in review databases in not desirable. Less than 50 percent of scientific journals were indexed in databases. Between the years studied, the scientific production of medical area of the country has been growing but to reach the proper situation, more effort is required.