A nuclear reactor is sometimes called an atomic pile because a reactor using graphite as a moderator consists of a pile of graphite blocks with rods of uranium fuel inserted into it. Reactors in which the uranium rods are immersed in a bath of heavy water are often referred to as "swimming-pool" reactors. Reactors of these types, in which discrete fuel elements are surrounded by a moderator, are called heterogeneous reactors. If the fissionable fuel elements are intimately mixed with a moderator, the system is called a homogeneous reactor (e.g., a reactor having a core of a liquid uranium compound dissolved in heavy water).

The breeder reactor is a special type used to produce more fissionable atoms than it consumes. It must first be primed with certain isotopes of uranium or plutonium that release more neutrons than are needed to continue the chain reaction at a constant rate. In an ordinary reactor, any surplus neutrons are absorbed in nonfissionable control rods made of a substance, such as boron or cadmium, that readily absorbs neutrons. In a breeder reactor, however, these surplus neutrons are used to transmute certain nonfissionable atoms into fissionable atoms. Thorium (Th-232) can be converted by neutron bombardment into fissionable U-233. Similarly, U-238, the most common isotope of uranium, can be converted by neutron bombardment into fissionable plutonium-239.

The transmutation of nonfissionable materials to fissionable materials in nuclear reactors has made possible the large-scale production of atomic energy. The excess nuclear fuel produced can be extracted and used in other reactors or in nuclear weapons. The heat energy released by fission in a reactor heats a liquid or gas coolant that circulates in and out of the reactor core, usually becoming radioactive. Outside the core, the coolant circulates through a heat exchanger where the heat is transferred to another medium. This second medium, nonradioactive since it has not circulated in the reactor core, carries the heat away from the reactor. This heat energy can be dissipated or it can be used to drive conventional heat engines that generate usable power. Submarines and surface ships propelled by nuclear reactors and nuclear-powered electric generating stations are in operation. However, nuclear accidents in 1979 at Three Mile Island and in 1986 at Chernobyl raised concern over the safety of reactors, and these concerns were revived somewhat in 2011 after an earthquake and tsunami resulted in a nuclear disaster in Fukushima, Japan. Another concern over fission reactors is the storage of hazardous radioactive waste. In the United States, the events at Three Mile Island made nuclear fission plants politically unacceptable and economically unattractive for many years; no new plants were approved for construction until 2012. In contrast, in France, Japan, and a few other nations nuclear fission has been used extensively for power generation, though the Japanese and French adopted a more cautious approach in the aftermath of Fukushima.