The beam energy may range from a few keV to several billion electron volts (BeV or GeV) depending on the design of the cyclotron. Charged particles such as protons, deuterons, α-particles, H⁻ etc. can be accelerated in a cyclotron. In some special cyclotrons, heavy ions like ^{3 2}S are also accelerated.

There are several features that distinctively characterize positive ion or negative ion cyclotrons. Negative ion cyclotrons need to be run under relatively higher vacuum than positive ion cyclotrons(~ 10⁻⁷ Torr vs 10⁻⁵ Torr), because H⁻ can lose electrons by encounters with any molecule during acceleration. The beam extraction efficiency in positive ion cyclotrons is ~ 80 % and the remaining 20 % is lost by interaction with the cyclotron housing inducing radioactivity. This warrants more shielding around these cyclotrons. In contrast, since negative ions are extracted with ~ 100 % efficiency and do not interact with the nucleus of any nuclide, the cyclotron housing is not activated, thus requiring less shielding. Targets can be bombarded internally at any radius of the positive ion cyclotrons for radionuclide production , whereas this is not possible in negative ion cyclotrons for lack of nuclear interaction of negative ions with target nuclei. In latter cyclotrons, the particle beam is intercepted with a thin carbon foil (~ 5 µm) toward the exit of the beam to strip two electrons from H⁻ forming an external proton (positive) beam to cause nuclear reactions in target nuclei. In positive ion cyclotrons, a deflector routes the particle beam outside for external irradiation of targets. A unique advantage of negative cyclotrons is that the particle beam can be split into two beams by placing one carbon stripping foil to cover only a part of the beam area and another foil at some distance away covering the remaining area. Thus, two same targets or two different targets can be irradiated simultaneously with the two beams to produce radionuclides .

Medical cyclotrons are compact negative ion cyclotrons that are commonly used for production of short-lived radionuclides such as ¹⁸F , ¹¹C , ¹³N , ¹⁵O , and so on used in positron emission tomography (PET) imaging. These nuclides are produced with low energy particles and hence the small size of the cyclotron that can be installed in a small room. In contrast, several medically-useful radionuclides such as ¹¹¹In, ⁶⁷Ga , etc. require high energy particles and so large cyclotrons, normally positive ion cyclotrons, are used for their production. The typical energy of the medical cyclotrons ranges between 3–18 MeV.

Some medical cyclotrons have provisions for acceleration of deuteron and H⁻interchangeably. Whereas high energy cyclotrons are shielded mostly by thick concrete walls, medical cyclotrons are self-shielded with lead blocks for reasons of compact nature. Four lead block quadrants are mounted on casters that wheel them in and out for closing and opening for easy access to service the cyclotron. Siemens, GE Healthcare, IBA, Best Cyclotrons, and Advanced Cyclotron Systems are the major manufacturers of medical cyclotrons in the USA.

When targets of stable elements are irradiated by placing them in the external beam of the accelerated particles or in the internal beam at a given radius inside a cyclotron, the accelerated particles interact with the target nuclei, and nuclear reactions take place. In a nuclear reaction, the incident particle may leave the nucleus after interaction with a nucleon, leaving some of its energy in it, or it may be completely absorbed by the nucleus, depending on the energy of the incident particle. In either case, a nucleus with excitation energy is formed and the excitation energy is disposed of by the emission of nucleons (i.e., protons and neutrons). Particle emission is followed by γ-ray emission when the former is no longer energetically feasible. Depending on the energy deposited by the incident particle, several nucleons are emitted randomly from the irradiated target nucleus, leading to the formation of different nuclides. As the energy of the irradiating particle is increased, more nucleons are emitted, and therefore a wider variety of nuclides is produced.

An example of a typical cyclotron-produced radionuclide is ¹¹¹In, which is produced by irradiating ¹¹¹Cd with 12-MeV protons in a cyclotron. The nuclear reaction is written as follows:

where ¹¹¹Cd is the target nuclide, the proton p is the irradiating particle, the neutron n is the emitted particle, and ¹¹¹In is the product radionuclide. In this case, a second nucleon may not be emitted, because there is not enough energy left after the emission of the first neutron. The excitation energy that is not sufficient to emit any more nucleons will be dissipated by γ-ray emission.

As can be understood, radionuclides produced with atomic numbers different from those of the target isotopes do not contain any stable (“cold,” or “carrier ”) isotope detectable by ordinary analytical methods, and such preparations are called carrier-free . In practice, however, it is impossible to have these preparations without the presence of any stable isotopes . Another term for these preparations is no-carrier-added (NCA) , meaning that no stable isotope has been added purposely to the preparations.

The target material for irradiation must be pure and preferably monoisotopic or at least enriched isotopically to avoid the production of extraneous radionuclides. Because various isotopes of different elements may be produced in a target, it is necessary to isolate isotopes of a single element; this can be accomplished by appropriate chemical methods such as solvent extraction, precipitation, ion exchange , and distillation. Cyclotron-produced radionuclides are usually proton-rich and therefore decay by β ⁺-emission or electron capture.