The research company of Atomic Energy of Canada LTD (AECL) operates 2 major nuclear energy research centres in Canada: Chalk River Nuclear Laboratories (CRNL), established during World War II on the Ottawa River some 200 km northwest of Ottawa; and Whiteshell Nuclear Research Establishment (WNRE) opened in 1963 beside Whiteshell Provincial Park, 105 km northeast of Winnipeg, Manitoba. Both conduct research and development on a wide variety of energy-related projects on behalf of AECL and under contract to outside companies and government bodies. At both sites reactor safety and the effects of radiation on living cells are studied. Test rigs which simulate the effects of system failures are used to ensure the correctness of safety codes and the effectiveness of safety-design features. Studies on the interaction of radiation and cells provide assurance that human safety is adequately protected by the codes and regulations.

Chalk River was the site of Canada's first large research reactor, NRX, a 10 megawatt (MW) facility which used natural uranium fuel and a deuterium moderator. Originally operated as a project of the National Research Council, CRNL became the main laboratory of AECL, the crown corporation established in 1952 to develop peaceful uses of nuclear energy. The Allies designed NRX to be an efficient producer of plutonium-239 for nuclear weapons; however, after WWII, CRNL turned its attention to research in other fields. NRX proved to be a uniquely powerful research tool and attracted worldwide attention to Chalk River in the postwar era. A complete technology evolved around the use of NRX and its later, more powerful companion, NRU. Designers of the Canadian nuclear power system, CANDU, relied heavily upon the experience at Chalk River, not least as a training ground for engineers and technologists from private-sector companies which would become suppliers of CANDU fuel and components (see Nuclear Power Plants).

Now these reactors also produce radioisotopes used for medical diagnoses and therapy. W. Bennett Lewis, CRNL's technical director 1946-76, left a lasting imprint on CRNL and on CANDU. Under his direction, the laboratories expanded from a wartime project of 200-300 professional and support staff to a world-class science centre, making important contributions to physics, chemistry, biology, nuclear technology and engineering. The new Tandem Accelerator Superconducting Cyclotron (TASCC) which was designed and built at CRNL will be a major Canadian facility for research in nuclear physics. Research in genetics illuminated the processes of repair in damaged living cells and shed new light on the genetic basis of susceptibility to cancer. Former Chalk River scientists and engineers are found in universities, industry and government services across Canada and the US. Devices and techniques developed at Chalk River, such as those for cancer therapy, neutron-activation analysis and radiation measurement, are in use around the world.

The Whiteshell research centre employs about 1000 scientists, engineers and support staff. An early project at WNRE was WR-1, a 40 MW research reactor, moderated with heavy water but cooled with a special, noncorrosive organic liquid (OS-84). It could achieve temperatures of 400°C without boiling. A demonstrator small reactor, designed to be a simple nuclear energy system for heating buildings and institutions, is now operating at WNRE. This reactor will be used to heat buildings there and such reactors could also generate electricity for remote communities. In collaboration with universities and federal and provincial authorities, WNRE devotes a very large effort to evaluating the disposal of hazardous waste such as the radioactive by-products of nuclear-power generation. Near WNRE is the Underground Research Laboratory, a dedicated geoscience research facility used for developing technologies relevant to nuclear-fuel-waste disposal.