Background and aim: Survey relation between h-index and self-citation and also their relation with another scientific performance evaluation indicators is important because when hirsch introduced it's index, has been considered self-citation too. Therefore this study survey effect of self-citation on quantitative and qualitative indicators of measuring the research output of faculty members in Isfahan University of medical sciences.

Material and methods: Research method is an analytical method conducted by using citation analysis technique. This study Population was scientific production of Isfahan University of medical science faculty member with h-index indicator (401 person) between 1996- 2013. Number of document, citation, number of citation without self-citation, h-index with and without self-citation and number of collaborators for each author was extracted from Scopus database. For data analyzing used descriptive and inferential statistics (Pearson test) and SPSS 18.

Findings: Based on research finding, cardiovascular research center had high mean in productivity indicator (45), number of citation (424/33) and h-index indicator (9.33). In self-citation index, health school and management and medical information was appropriated high (24.44) and lower (0.66) rate of self-citation respectively. There was significant relation between total number of citation and self-citations, author received citation number and collaboration with other author, author self-citation number and collaboration with other, h-index and author self-citation and also author self-citation and productivity.

Conclusion: In this study, between self-citation and total quantitative and qualitative indicators in measure scientific production there was significant relation. Therefore, this task needs solutions that can decrease effect of self-citation on research performance evaluation indicators of scientific parameters production.