The Population Health Research Institute (PHRI) provides a forum for the conduct of large international clinical trials, population health studies, and studies in outcomes research. While its primary role is to provide leadership in international health research, the PHRI also plays an active role in the education of individual researchers, and in building capacity internationally for the development of global research programs.

The Farncombe Family Digestive Health Research Institute is an integrated group of clinical and basic scientists dedicated to understanding the causes of chronic digestive diseases. The institute is focused on developing new strategies for the diagnosis, treatment and prevention of intestinal diseases such as Crohn’s disease and colitis, which will have global benefits.

McMaster is home of Canada's only gnotobiotic, or germ free, research facility for gastrointestinal disease and other research including immunology and microbiology. The $5 million Farncombe Family Gnotobiotic Facility, located at the Health Sciences Centre, was opened in 2005. The 3,000-square-foot laboratory's strict controls ensure sterility and control of the bacterial environment for research into the host-microbial interaction in the gut, a significant issue for understanding immune reactivity in the gut and susceptibility to a range of gastrointestinal and other diseases such as inflammatory bowel and functional bowel diseases, allergy and autoimmunity including diabetes.

The Firestone Institute for Respiratory Health is a world class respiratory program providing comprehensive patient care, research and education. The program is comprised of an outpatient service, an inpatient unit managing severe or chronic respiratory diseases and the regional thoracic (chest) surgery program.

The Thrombosis and Atherosclerosis Research Institute developed from the former Henderson Research Centre, which was established in 1988 as a joint initiative of the Hamilton Civic Hospitals (now part of the Hamilton Health Sciences) and McMaster University. Its mission is "To conduct research into the pathogenesis, prevention, diagnosis and treatment of thrombosis and vascular disease and to provide a resource for key areas of research as outlined in the mission statement of the Hamilton Health Sciences."

As a result of the DeGroote family gift, a world-class institute will be created at McMaster to focus the clear, piercing light of science and medicine on this age-old problem. Encompassing an array of technologies, disciplines and specialties, the institute will explore the causes of a number of different types of pain, develop new strategies for its prevention, diagnosis and management and develop innovative care for patients.

The mission of AllerGen (Allergy, Genes and Environment Network) is to catalyze and support discovery, development, networking, capacity building, commercialization and knowledge translation that contribute to reducing the morbidity, mortality and socio-economic burden of allergic and related immune diseases.

The Brain-Body Institute (BBI) is a joint research initiative between St. Joseph's Healthcare, Hamilton, and McMaster University and was created to advance the understanding of relations between the brain, the nervous system and bodily disorders. Clinical and basic scientists in this multidisciplinary Institute study the interaction and impact of environmental factors, including stress, early life experiences and early microbial exposure on the brain and nervous system.

CLARITY represents the formal alliance of a group of researchers who have enjoyed a long-standing and fruitful collaboration. The seven CLARITY faculty members — Gordon Guyatt, Brian Haynes, Deborah Cook, Maureen Meade, PJ Devereaux, Holger Schünemann and Mohit Bhandari — participated in an inaugural group meeting in 2003. Through formal collaboration, Clarity's clinical advances through research and information translation has been pivotal in creating a renewed sense of spirit, vision and commitment.

The Centre for Evaluation of Medicines is a multi-disciplinary resource that provides expertise in clinical pharmacology and toxicology, economics, health policies, behavioral sciences, information technology, research design and biostatistics. The CEM is a neutral and objective source for information and leading edge analyses in the fields of therapeutics and health policy interventions.

The Hamilton Centre for Kidney Research (HCKR) is directly affiliated with the Department of Medicine’s Division of Nephrology located at St. Joseph's Healthcare. The mandate of the HCKR is to combine expertise in clinical and basic research to reduce the risk of kidney disease and its complications.

The Health Information Research Unit (HIRU) conducts research in the field of health information science and is dedicated to the generation of new knowledge about the nature of health and clinical information problems, the development of new information resources to support evidence-based health care, and the evaluation of various innovations in overcoming health care information problems.

The McMaster Transfusion Research Program (MTRP) is a joint partnership between the Canadian Blood Services (CBS) and McMaster University, Faculty of Health Sciences. MTRP is dedicated to the advancement of innovative evidence-based diagnostic, clinical, and therapeutic practices in Transfusion Medicine. Their ultimate goal is to provide scientific evidence that will inform transfusion practice and enhance the safety of blood recipients.

The St. Peter’s Centre for Healthy Aging is affiliated with both Hamilton Health Sciences and McMaster University's Department of Medicine. They are committed to the development and testing of methodologies for the assessment and treatment of dementia, the education and promotion of the elderly, of individuals' rights and autonomy, and of ethical medical practice.

The Geriatric Education and Research in Aging Sciences (GERAS) Centre is uniquely positioned to be a leader in successful aging in Hamilton, Ontario. In partnership with St. Peter’s Hospital and McMaster University, this centre is strong in its collaborative team-based care delivery with access to leading geriatric medicine specialists and psychiatrists, interprofessional teams, and a concentrated ambulatory practice. The GERAS Centre is committed to educating and empowering seniors to regain and retain independence and to manage their health through active participation in their care. These new models of care engage family members and build capacity for support within the community. The experts at St. Peter’s are also dedicated to advancing health care education for the present and next generation of health care professionals. Through innovative research the GERAS Centre will close the gap between knowing and doing to contribute to improved quality of life for seniors.