Introduction: One of the most important criteria for assessment of research activities is the quantitative evaluation of scientific output, for which the most effective method is the assessment of indexed articles in valid databases. This study aimed at mapping the scientific output of indexed thyroid disease in the Web of Science database between 2007-2013. Materials and Methods: For the present study, we conducted an analytical survey, using a scientometric approach. The study population included all populations of scientific publications on indexed thyroid diseases in the web of science database between the years 2007-2013. Data were analyzed by Excel software, and the scientometric tool “HistCite” was used for mapping of scientific output in the region. Results: Our findings showed that from the 2294 records retrieved, 7344 authors affiliated to 1339 institutions, had published their research in 700 journals, using 6 document types. The Thyroid journal had the largest number of local and global citations. Majority of scientific productions in the Middle-East belonged to Turkey and Iran, i.e. 60.7%, 17% respectively. In the scientific map, 5 scientific clusters were developed based on TGCS and TLCS. Conclusion: According to the results, Iran, in the field of thyroid disease, Iran with a rate of 17%, ranked as the second country in the middle-east in scientific publications, a relatively low ranking with regard to the significance of thyroid disease. To increase the scientific output in Iranian universities and research facilities, precisely designed strategies are urgently needed, based on which Iranian researchers in this field can achieve top rankings with research output in the Middle-East in the near future.