The University of Otago is one of the two largest research institutions in New Zealand, second only to the University of Auckland. In the professional rankings of New Zealand universities, the University of Otago has multiple top ranked majors: Biomedical, Clinical Medicine, Earth Sciences, Economics, Education, English Language and Culture, History and Classics, Law, Philosophy, Public Health, Religious Studies and Theology, Sports and Sports Science. Among them, the medical profession is world-renowned.

Most of the research topics at the University of Otago focus on health science, including asthma and respiratory disorders, cardiovascular endocrinology, functional genomics, gene expression and proteomics, foundational diseases and immune protection in immunology, structure and function of the nervous system, oral microbiology and dental health, oxidative stress in health and disease, public health, formulation and administration, and virology. Many of these research projects are at the world's leading level.