Research is one of the strongest components of Alagappa University. All the faculty members of the University have been actively engaged in research. With financial support from national/international agencies like DST, DBT, UGC, CSIR, ICMR, DRDO, MHRD, UNESCO, etc., various research projects are being carried out. Currently 70 projects with external funding to the tune of Rs.1400 lakhs are on-going. The University Grants Commission has been supporting the Departments of Physics, Chemistry, Biotechnology, Bioinformatics -(DST-FIST) and Physical Education under Special Assistance Programme (SAP).

Similarly, the Department of Science and Technology (DST), Ministry of Science and Technology, Government of India has been supporting the Departments of Physics, Chemistry and Biotechnology under "Fund for Improvement of S&T Infrastructure in Universities and Higher Educational Institutions (FIST)" scheme. Based on the research publications and 'h' index, the DST has recently sanctioned a research grant of Rs.600 lakhs to all the Science Departments of the University under Promotion of University Research and Scientific Excellence (PURSE) scheme.

The average impact factor of the publications made is close to 2.0. Alagappa University has published 618 research papers with an average citation per paper of 2.85 during the period 1999-2008 and has a high share (31.07%; All India Rank 3 among top 53 Indian Universities) of International Collaborative Publications in total publications output during the same period (Gupta BM, Indian J. Sci. Technol. 3(7):837-843, 2010). Based on the average H-index of 22, Alagappa University has got 27th rank at the national level.

Apart from earmarking Rs. 1000 lakhs for equipments and consumables in the last 5 years, the University has created an internal research fund, Alagappa University Research Fund (AURF) with a corpus, of Rs. 500 lakhs for inculcating research culture and promoting research. Every year, projects worth Rs. 50 lakhs are sanctioned by the University from its own funds for research.

A separate Research Section has been functioning under the Dean of Research since 24th January, 2011. The University has Research Advisory Committee (RAC) to monitor and foster research activities at various levels in the University with the University's objective of 'Fostering Research for the Advancement and Dissemination of Knowledge' utmost in mind. The RAC has formulated the guidelines for admission to M.Phil and Ph.D. programs.

Alagappa University is one of the early birds to adopt the University Grants Commission (Minimum Standards and Procedures for award of M.Phil and Ph.D. Degree) Regulations, 2009. The guidelines were formed on the lines of UGC regulations as well as on the guidelines of Tamil Nadu State Council for Higher Education (TANSCHE) in important Aspects such as fixing the eligibility criteria for M.Phil/Ph.D Supervisor-ship, Procedure for admission, Allocation of Research Supervisor to Research Scholars, Course Work, Evaluation and assessment methods. On the advice of RAC, the University conducts an All India Level Pre-PhD Entrance Examination twice a year(February and July) for selecting meritorious candidates for M.Phil and Ph.D. programs in various disciplines.

Wide publicity is also given through National dailies and University website for the Pre-PhD Qualifying Entrance Examination. The RAC also advises the University authorities in several other matters which are involved with fostering of research and maintaining the quality of the research programs. The RAC meets 4-6 times in a year and evolves strategies for maintaining quality in research besides dealing with special issues, as they may arise and provides recommendation based on merits of each case.

The University had thus far enrolled 3796 candidates for doctoral programs, of whom 1867 got awarded the PhD and remaining candidates pursue their work.