Robert K. Merton has made up the expression of “Matthew effect" in sociology of Science that explains how the eminent scientists frequently get more acknowledgment than unknown researchers, even if their work was similar. The objective of this study is to analyze and visualize the influence of “Matthew effect" on the quantitative (papers) and qualitative (citations) of scientific publications originated by Iranian Medical Sciences Universities throughout 2002 – 2006. The method of current study was an analytical-descriptive review. All data about publications originated by Iranian Medical Sciences Universities were extracted from the database of Web of Science (WoS). The citations received by Medical Sciences Universities were extracted from the Citation Report. The relationship between the publications and citations was plotted by Excel. We found a non-linear correlation between the publications and citations of Iranian Medical Universities. The first class and other universities group showed a positive impact related to the Matthew effect; whereas this relationship among second class universities and third class universities were negative. Tehran University of Medical Sciences got the first place on the ranking order based on the scale independent indicator while Bushehr Medical Science University was the last one. Analysis of data indicated that there was a non-liner relationship between Iranian scientific profiles and the citations that they received. The Scale-independent Indicators were the most reliable metrics for normalizing the ranking of universities.