Molecules are electrically neutral groups of two or more atoms bound together by chemical bonds. Molecules are distinguished from ions by lack of charge. However, in quantum physics, organic chemistry and biochemistry, the term "molecule" is often used loosely, and it is also applicable to polyatomic ions.

In the theory of gas dynamics, the term molecule is usually used for any gaseous particle, regardless of its composition. According to this definition, noble gas atoms are considered molecules because they are monatomic molecules.

A molecule may be homonuclear, that is, it consists of atoms of a chemical element, just like oxygen (O2). It can also be heteronuclear, a compound consisting of more than one element, such as water (H2O). Atoms and complexes linked by noncovalent interactions, such as hydrogen or ion bonds, are not generally considered to be monomolecular.

Molecules are common in organic matter as components of matter (and therefore Biochemistry). They also make up most of the ocean and atmosphere. However, most of the familiar solid materials on earth, including the crust, mantle and core minerals, contain many chemical bonds, but are not made up of recognizable molecules. Similarly, although ionic crystals (salts) and covalent crystals (network solids) are usually composed in planar (for example, graphene) or three-dimensional (for example, in diamonds, quartz or sodium chloride). The theme of repetitive cellular structure is also applicable to most condensed phases with metal bonds, which means that solid metals are also not composed of molecules. In glass, atoms can also be bound together by chemical bonds. There are no definable molecules, and there is no regularity of repeated units to characterize the crystal.