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The application of currently available sophisticated algorithms of citation analysis allows for the incorporation of the "quality" of citations in the evaluation of scientific journals. We sought to compare the newly introduced SCImago journal rank (SJR) indicator with the journal impact factor (IF). We retrieved relevant information from the official Web sites hosting the above indices and their source databases. The SJR indicator is an open-access resource, while the journal IF requires paid subscription. The SJR indicator (based on Scopus data) lists considerably more journal titles published in a wider variety of countries and languages, than the journal IF (based on Web of Science data). Both indices divide citations to a journal by articles of the journal, during a specific time period. However, contrary to the journal IF, the SJR indicator attributes different weight to citations depending on the "prestige" of the citing journal without the influence of journal self-citations; prestige is estimated with the application of the PageRank algorithm in the network of journals. In addition, the SJR indicator includes the total number of documents of a journal in the denominator of the relevant calculation, whereas the journal IF includes only "citable" articles (mainly original articles and reviews). A 3-yr period is analyzed in both indices but with the use of different approaches. Regarding the top 100 journals in the 2006 journal IF ranking order, the median absolute change in their ranking position with the use of the SJR indicator is 32 (1st quartile: 12; 3rd quartile: 75). Although further validation is warranted, the novel SJR indicator poses as a serious alternative to the well-established journal IF, mainly due to its open-access nature, larger source database, and assessment of the quality of citations.