An exotic atom is an otherwise normal atom in which one or more sub-atomic particles have been replaced by other particles. For example, electrons may be replaced by other negatively charged particles such as muons (muonic atoms) or pions (pionic atoms). Because these substitute particles are usually unstable, exotic atoms typically have very short lifetimes and no exotic atom observed so far can persist under normal conditions.

In a muonic atom (previously called a mu-mesic atom, now known to be a misnomer as muons are not mesons), an electron is replaced by a muon, which, like the electron, is a lepton. Since leptons are only sensitive to weak, electromagnetic and gravitational forces, muonic atoms are governed to very high precision by the electromagnetic interaction.

Since a muon is more massive than an electron, the Bohr orbits are closer to the nucleus in a muonic atom than in an ordinary atom, and corrections due to quantum electrodynamics are more important. Study of muonic atoms' energy levels as well as transition rates from excited states to the ground state therefore provide experimental tests of quantum electrodynamics.

Other muonic atoms can be formed when negative muons interact with ordinary matter. The muon in muonic atoms can either decay or get captured by a proton. Muon capture is very important in heavier muonic atoms, but shortens the muon's lifetime from 2.2 μs to only 0.08 μs.

Muonic hydrogen is like normal hydrogen with the electron replaced by a negative muon, which is to say, a proton orbited by a muon. It is important in addressing the proton radius puzzle.

Muonic hydrogen atoms can form muonic hydrogen molecules. The spacing between the nuclei in such a molecule is hundreds of times smaller than in a normal hydrogen molecule –so close that the nuclei can spontaneously fuse together. This is known as muon-catalyzed fusion, and was first observed between hydrogen-1 and deuterium nuclei in 1957. Muon-catalyzed fusion has been proposed as a means of generating energy using fusion reactions in a room-temperature reactor.

The symbol ^4.1H (Hydrogen-4.1) has been used to describe the exotic atom muonic helium (⁴He-μ), which is like helium-4 in having two protons and two neutrons. However one of its electrons is replaced by a muon, which also has charge –1. Because the muon's orbital radius is less than ⁠1/200th⁠ the electron's orbital radius (due to the mass ratio), the muon can be considered as a part of the nucleus. The atom then has a nucleus with two protons, two neutrons and one muon, with total nuclear charge +1 (from two protons and one muon) and only one electron outside, so that it is effectively an isotope of hydrogen instead of an isotope of helium. A muon's weight is approximately 0.1 Da so the isotopic mass is 4.1. Since there is only one electron outside the nucleus, the hydrogen-4.1 atom can react with other atoms. Its chemical behavior is more like a hydrogen atom than an inert helium atom.

A hadronic atom is an atom in which one or more of the orbital electrons are replaced by a negatively charged hadron. Possible hadrons include mesons such as the pion or kaon, yielding a pionic atom or a kaonic atom (see Kaonic hydrogen), collectively called mesonic atoms; antiprotons, yielding an antiprotonic atom; and the Σ⁻
particle, yielding a Σ⁻
or sigmaonic atom.