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Siddha Medicine was established in 1929 along with Ayurveda and Unani under the College of Indigenous Medicine, at Borella. The Board of Indigenous Medicine awarded Diploma in Indigenous Medicine and Surgery (DIMS) until 1961. After the implementation of Ayurveda act No 31 of 1961 the name of the degree was changed to Diploma of Ayurvedic Medicine and Surgery (DAMS).

The College of Ayurvedic Medicine was upgraded to the status of Institute of Indigenous Medicine and affiliated to University of Colombo on 2nd April 1976. A curriculum workshop was held in 1983 to formulate the curriculum for degree courses and the senate, University of Colombo approved it. The Degree to be conferred on Siddha Medicine is Bachelor of Siddha Medicine and Surgery (BSMS) since 1983.
After the ethnic disturbances occurred in 1983, the Siddha section was transferred from the University of Colombo to the University of Jaffna on 2nd July 1984 and was accommodated under the Faculty of Arts as a Department. The Department of Siddha Medicine commenced its academic functions at Kaithady which is 11km away from the University of Jaffna.
The Department of Siddha Medicine became a separate Unit under the direct administration of the Vice-Chancellor since 1st October 1993. A proposal was given to the UGC to upgrade the Unit as Faculty / Institute.
Siddha Medical course comprises lectures, practical and clinical studies. The location of the Government Ayurvedic Hospital in the adjoining compound is more appropriate to carry out the clinical program. The Unit has enough land space for expansion programs and infrastructure development.