Research
- Center for Applied Ethics – established on July 1, 2002 under the administration of Rev. Fr. Tamerlane R. Lana, O.P., The Center was the flagship project of the University towards achieving its vision of becoming the "Center for Contextualized Theology in Asia by 2011."
- Center for Conservation of Cultural Property and Environment in the Tropics – envisions to be a leading center and prime mover in the promotion of Cultural Heritage in the Philippines by providing and developing professional and academic expertise in conservation and heritage management of cultural properties in the tropics.
- Center for Educational Research and Development – was established in June 1979, by Rev. Fr. Paul P. Zwanepoel. Through the years, the Center has evolved from being an academic arm of the various colleges in the university providing educational, research and consultancy services to a research-intensified unit thus, redefining the concept of the university faculty as producers of knowledge and information.
- Center for Intercultural Studies – was opened as the Chiang Ching-kuo Centre for Intercultural Studies in 1993 in the Main Building during the term of Rev. Fr. Rolando de la Rosa, O.P. as Rector of the University with Dr. Alfredo Co as the first Director of the Centre.
- Center for Research on Movement Science – naugurated on February 21, 2003,The Center for Research on Movement Science envisions itself to become an acknowledged expert in the country, in the field of research on exercise and human movement through the Human Performance Laboratory and the Biomechanics Laboratory.
- Research Center for the Natural Sciences – the venue for science and technology research in the University of Santo Tomas. Established in 1962, it was originally conceived as the University Research Center, encompassing both the cultural and the experimental sciences. However, in the succeeding years, it gradually assumed an orientation towards the natural sciences.
- Social Research Center – Established on December 1, 1979, Social Research Center (SRC) is the university's research arm for the social sciences.
- UST Psychotrauma Clinic
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