Clathrates are divided into two broad classes depending on the properties of the host compound. Molecular clathrates are formed by "hosts" with intramolecular cavities (Fig. a); such clathrates can exist both in a solution and in the crystalline state. If the "host" can form only intermolecular or crystal cavities, then it can produce lattice clathrates (Fig. b), which are stable only in solid state.

In all clathrates weak intermolecular bonds (either van der Waals or hydrogen) are formed between the "hosts" and the "guests". Clathrates are non-stoichiometric compounds in which the ratio between the numbers of "guest" and "host" molecules is not necessarily an integer, e.g. Cl₂·5.75H₂O.

An important example of a lattice clathrate is methane hydrate, in which methane molecules are physically trapped in cavities of the crystal lattice of ice. This compound is widespread in nature; reserves of methane on the ocean floor are likely to significantly exceed the reserves of this gas in the free state.

Formation of clathrates is used in chromatography, for storage of highly toxic substances and gases, sea water desalination and separation of compounds which have similar properties but differ in the geometry of molecules, e.g. cis-trans hydrocarbons. Currently, there are a lot of studies focused on the possibilities of applying water-based clathrates and metal frames for hydrogen accumulation and storage.