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One type of frequently used references in scientific papers is online references. The aim of this study is to study the prevalence, accessibility and types of online sources in biomedical journals in Iran from 2010 to 2012. We analyzed online references cited in 401 articles from 21 scientific journals indexed in PubMed, Web of Science, and Scopus. Findings revealed that only 73 papers (18.2%) had cited online sources in their references. of 186 online citations, 72 (38.7%) citations were accessible, and the URLs to 114 citations did not work (61.3%). The majority of unreachable citations were unstable citations (32.3%). Most online sources (62%) were cited in “Iranian Journal of Public Health”. An increase in the number of online citations was observed over the studied years. The study indicated that the rate of online citations is low in the studied journals, and most online citations were unreachable. The lack of clear guidelines in citing online sources seemed to be a major reason for the inaccessibility of online citations.