A clathrate or clathrate compound or cage compound is a chemical substance consisting of a lattice of one type of molecule trapping and containing a second type of molecule. (The word comes from the Greek klethra, meaning "bars" (in the sense of a lattice).) For example, a clathrate hydrate involves a special type of gas hydrate that consists of water molecules enclosing a trapped gas. Prospectors believe that compounds on the sea bed have trapped large amounts of methane in similar configurations. Researchers have begun to investigate silicon clathrates for possible semiconducting and superconducting properties.

A clathrate therefore is a material which is a weak composite, with molecules of suitable size captured in spaces which are left by the other compounds. They are also called host-guest complexes, inclusion compounds, and adducts (chiefly in the case of urea and thiourea). They used to be called "molecular compounds".

In 1945, H. M. Powell named these compounds clathrate, which means "locked" in Greek. Clathrate complex used to refer only to the inclusion complex of hydroquinone, but recently it has been adopted for many complexes which consist of a host molecule (forming the basic frame) and a guest molecule (set in the host molecule by interaction). The clathrate complexes are various and include, for example, strong interaction via chemical bonds between host molecules and guest molecules, or guest molecules set in the geometrical space of host molecules by weak intermolecular force. Typical examples of host-guest complexes are inclusion compounds and intercalation compound.

The history of clathrate compounds is relatively new. Their study was begun by P. Pfeiffer in 1927. In 1930, E. Hertel defined molecular compounds as substances decomposed into individual components following the mass action law in solution or gas state. Therefore, basic information about clathrate compounds (then called molecular compounds) was known in those days. The development of clathrate compounds was attained by analyzing crystal structure by Powell (mentioned above), and they were applied to the separation of paraffin using a urea or thiourea host. Thereafter, cyclodextrin , crown ether, and cryptand were found as host molecules (see figure).

In analyzing and separating techniques, the concept of inclusion compounds has taken root and many applications of them are known. It is possible to isolate not only chemically different species but also structural isomers, positional isomers (enantiomers and diastereomers), and radioactive isomers using clathrate compounds.