This research was conducted to evaluate the structure and content of electronic databases of Iranian journals. The population included Sid, Magiran and Namamatn databases. To review the structure of the target databases, data were gathered by a checklist and to review the content of them, the database managers were interviewed and some aspects of the databases were observed. The compatibility rate of Sid, Magiran, and Namamatn with the structure criteria were 50.43%, 54.70%, 41.88%. respectively. Findings showed that the coverage of Magiran, in comparison with all the Iranian journals, and the Sid, in comparison with scientific and research journals, were more comprehensive (36.35%, and 94% respectively). The databases subject coverage was reviewed and it was revealed that Sid database was rich in medical and paramedical subjects but Magiran and Namamatn databases included more journals in human sciences. Contrary to Sid and Magiran, and because of using a controlled indexing language, Namamatn database had a more clear and consistent procedure for indexing. The traditional overlap of the databases was calculated. The most overlap was observed between Magiran and Sid databases (with 23.82%) and the least one was between Sid and Namamatn databases (with 0.67%). Overall overlap of the three databases was calculated 5.12%. Relative overlap was also measured and findings showed that the most overlap was in Sid (45.15%), and the least one was in Magiran (10.47%).