A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and molecule is often used when referring to polyatomic ions.

A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O₂); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H₂O). In the kinetic theory of gases, the term molecule is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not considered single molecules.

Concepts similar to molecules have been discussed since ancient times, but modern investigation into the nature of molecules and their bonds began in the 17th century. Refined over time by scientists such as Robert Boyle, Amedeo Avogadro, Jean Perrin, and Linus Pauling, the study of molecules is today known as molecular physics or molecular chemistry.

According to Merriam-Webster and the Online Etymology Dictionary, the word "molecule" derives from the Latin "moles" or small unit of mass. The word is derived from French molécule (1678), from Neo-Latin molecula, diminutive of Latin moles "mass, barrier". The word, which until the late 18th century was used only in Latin form, became popular after being used in works of philosophy by Descartes.

The definition of the molecule has evolved as knowledge of the structure of molecules has increased. Earlier definitions were less precise, defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties. This definition often breaks down since many substances in ordinary experience, such as rocks, salts, and metals, are composed of large crystalline networks of chemically bonded atoms or ions, but are not made of discrete molecules.

The modern concept of molecules can be traced back towards pre-scientific and Greek philosophers such as Leucippus and Democritus who argued that all the universe is composed of atoms and voids. Circa 450 BC Empedocles imagined fundamental elements (fire (), earth (), air (), and water ()) and "forces" of attraction and repulsion allowing the elements to interact.

A fifth element, the incorruptible quintessence aether, was considered to be the fundamental building block of the heavenly bodies. The viewpoint of Leucippus and Empedocles, along with the aether, was accepted by Aristotle and passed to medieval and renaissance Europe.

In a more concrete manner, however, the concept of aggregates or units of bonded atoms, i.e. "molecules", traces its origins to Robert Boyle's 1661 hypothesis, in his famous treatise The Sceptical Chymist, that matter is composed of clusters of particles and that chemical change results from the rearrangement of the clusters. Boyle argued that matter's basic elements consisted of various sorts and sizes of particles, called "corpuscles", which were capable of arranging themselves into groups. In 1789, William Higgins published views on what he called combinations of "ultimate" particles, which foreshadowed the concept of valency bonds. If, for example, according to Higgins, the force between the ultimate particle of oxygen and the ultimate particle of nitrogen were 6, then the strength of the force would be divided accordingly, and similarly for the other combinations of ultimate particles.