The concept of clathrate compound [1] has been one of major discoveries in chemistry. Originally, it was concentrated on spatial fit between the host and guest components. Soon a physicochemical rationale for defining the stability conditions for clathrate formation was reported [2]. The term clathrate is in frequent use in contemporary scientific literature [3]. There are, however, many ambiguities concerning the appropriate use in different structural situations. At the 1st International Symposium on Clathrate Compounds and Molecular Inclusion Phenomena (Jachranka-Warsaw, 1980) Weber and Voegtle, have presented a proposal for more adequate nomenclature of inclusion compounds. They have suggested two main improvements: (a) structural one, defining more precisely the geometry of inclusion (cage, tubular etc.) and (b) interaction type guest-host, using ‘clathrate’ for systems without any chemical interactions and ‘complex’ for any other. Taking into account frequent use of the term clathrate, intended mostly as description of mutual geometrical interaction between the components, an advanced nomenclature system would be welcome in order to precisely define the compounds, both structurally and from interaction point of view. Geometric part of the problem seems rather straightforward (clear description of the host structure) but it may contain specific difficulties related to mutual relationship betwen the host and guest. The same host structure may be of cage type (guest species of adequate size and shape) or zeolite-type (small guest species) or, in some cases, tubular/layered for long chain or planar guest molecules. Chemical interactions guest-host should conveniently be described in the compound’s name. The general term ‘complex’ is certainly adequate but may be replaced by more specific terms. The term ‘metallic’ would be appropriate for clathrate type structures having metallic type bonding of the guest species (Zintl phases), ‘hydrogen bonded’ for clathrates containing hydrogen bonds guest-host (in addition to the main clathrate type characteristics), covalent or coordination for respective ‘complex’ type clathrates, and ionic for inclusion compounds of, say, cationic species in t he anionic host (e.g. water/halogenide). Structures, called sometimes semiclathrate, in which functional groups of the guest participate in the host framework, maybe ionic or neutral, depending on the nature of the guest. In the present paper a novel nomenclature system will be presented and illustrated by respective examples. Evolution of the concept from ‘clathrate’through ‘organic zeolite’ to ‘Metal Organic Framework’ and ‘Covalent Organic Framework’, with the emphasis on the physicochemical properties as related to the crystal structure.