Purpose: This research studies traditional overlap, relative overlap and synthetic freedom in the databases PubMed and Web of Science (WoS) in 'Endocrine System Diseases' area.Methodology: Research population of this descriptive survey consists of all retrieved articles on endocrine glands in PubMed and WoS in 2009. The search was done using 11 major descriptors from Medical Subject Headings (MeSH). Data analysis was performed using endnote and Excel. Different overlaps including (subject, title, and information resources) and traditional and relative overlaps for each descriptor were calculated. Findings: Among 7389 articles retrieved in both databases, 4177 and 3212 titles belonged to PubMed and WoS, respectively, 2586 ones were in both databases, 1591 articles were unique to the PubMed database and 626 titles were unique in WoS. It was also found that traditional overlap between the two databases is 53.84%, and relative overlap percentage of PubMed, 80.51, is more than WoS with 61.91%.Conclusions: The findings showed that there is a high overlap between the two databases. Accordingly, considering the current limitations and since the PubMed is free of charge, it can be a suitable substitute for WoS database. This avoids the increased subscription fee, and helps libraries subscribe other databases which can be as supplement of PubMed.