A clathrate is a solid material in which small molecules of one substance (called the guest molecules) are trapped and enclosed in spaces in the crystal lattice of another substance (called the host molecules). The word comes from the Latin clathratus meaning "furnished with a lattice." Clathrates are sometimes called cage compounds or enclosure compounds.

Methane hydrate, for example, is a clathrate in which methane molecules, typically released by bacterial decay, become caged within the open-structured lattice of water ice. It is found commonly in permafrost regions in Siberia and North America and is widespread on the seafloor in the vicinity of continents. The release of methane from these reserves, as the ice melts, has been cited as a potentially significant factor in globally warming. Methane hydrate is also among the clathrate hydrates that have been identified in the ice of cometary nuclei. Quinol is another substance that forms a variety of clathrates with substances such as xenon and sulfur dioxide.

Researchers have begun to investigate silicon and germanium clathrates for possible semiconducting and superconducting properties.