Research activities at the Faculty are organized via the Organizational Unit for Research and Health Care Work, which is made up of teachers, associates and other research staff. In the recent past, high quality equipment for molecular research was purchased for its labs, and ultrastructural research is done on somewhat older equipment for electronic microscopy. The Faculty invested a lot in 2006/2007 in the equipment for dual purposes (education & research) or for research only, as well as in the construction, renovation and adaptation of the space for these activities. In its research activity the Faculty includes both PhD and M.Sc candidates and undergraduate students.

There is a significant number of projects performed at the Faculty in basic, applied, innovative and developmental research. In the period 2000/2005 the Ministry of Science of the Republic of Serbia funded 20 projects with 85 researchers. At the moment, 84 teachers and associates of the Faculty are engaged in various projects.

Teachers and associates improved their knowledge and expertise in various research & educational & health care centres in our country and abroad. There have been over 260 study/training visits abroad, and over 160 trainings in the regional & national centres. Reknown experts and teachers in various fields of biomedical sciences have been elected visiting professors of the Faculty. Co-operation with the Centre for Oncologic Prevention in Florence, Universities in Sofia, Belgorod and Geteborg, as well as the participation in the NIH USA, TEMPUS and other international projects, have a special place in the strategy of quality assurance in research activities of the Faculty.

Teachers and associates of the Faculty have published so far 866 papers referred to in the MEDLINE/PUBMED data base, out of which 395 are in the SCI list. In the period 2006/07 there were 401 published papers, with 85 from the SCI list.

The Faculty itself publishes three scientific journals, and its teachers are editors of the university journal in the field of medicine.

There has been 663 M.Sc  theses and 518 PhD dissertations defended at the Faculty.

The Centre for Quality Control, takes care of the research activities at the Faculty  and that domain is regulated by the pertinent documents of the Ethics Committee of the Faculty.

Periodic reports on the results of research activities, as well as the research programs and plans, are submitted to the Assembly for Education and Science of the Faculty.
Based on the analysis of the research conditions fulfillment, the Ministry of Science and Environmental Protection adopted the Decision on the Accreditation of the Faculty of Medicine in Nis for Research. The competences of its researchers and verification of standards and results make possible for the Faculty of Medicine in Nis to be included into the European area of higher learning and modern research programs.