A molecule is usually defined as a structure consisting of two or more atoms bound together. A molecule may consist of two or more atoms of the same element—as in hydrogen, sulfur, and phosphorus molecules, for example. On the other hand, a molecule may be made up of atoms of two or more different elements, in which case it constitutes the smallest subdivision of a chemical compound, such as water. Some molecules, such as those of certain proteins, contain many thousands of atoms.

A molecule is sometimes defined—especially by chemists—as the smallest part of an element or compound that can exist alone and still retain the properties of the element or compound. By this definition, the atoms of certain elements (for example, helium and neon) are molecules. Such molecules are termed monatomic.