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• Introduction: Scientometric indicators are used for measuring and evaluating the quality and quantity of scientific productions in the scale of individuals as well as institutions. The database of Web of Science (WOS) is one of the most prestigious international databases for analyzing scientific publications. This study aimed to determine the relationship between qualitative and quantitative indicators of scientific productions originated by Iranian universities of medical sciences indexed in WOS during 1999-2008. • Methods: Using an analytical method, the quality and quantity indicators of publications originated by Iranian universities of medical science were analyzed. Data collection tools were the checklists that we designed in Microsoft Excel. The validity of the checklists was verified by experts. All dissimilar forms of university names were retrieved via Hist-Cite software. The search strategy was conducted based on the obtained various universities names in the WOS database. A total number of 15856 documents were retrieved. SPSS16 was used to analyze the data. Kruskal-Wallis and Spearman tests were used to calculate the chi-square values. • Results: Analysis of data indicated a significant difference among three types of universities of medical sciences in the term of quantitative and qualitative indicators. Moreover, the Spearman tests showed a positive and significant correlation between quantitative and qualitative indicators. • Conclusion: The study indicated that the universities which produced a greater number of scientific productions also had more favorable conditions in the term of quality attributes such as citations and H-index. This may suggest that the universities have taken into consideration not only the quantitative but also the qualitative aspects of publications. • Keywords: Scientometrics; Databases; Citation.