This paper reports new inclusion complexes of furaltadone [5-(morpholinomethyl)-3-[(5-nitrofurfurylidene)-amino]-2-oxazolidinone] hydrochloride with acetic acid, propionic acid, and water as substrate molecules. The inclusion compounds crystallize in the monoclinic space group P21/c (Z = 4) and represent channel-type clathrates in which the guest molecules are accommodated in continuous canals running through the crystal parallel to the c axis. The canals have an approximately cylindrical shape and are lined with oxygen and chlorine nucleophiles; nevertheless, the enclathrated species are translationally disordered in their location in the channel. The crystal structures of the inclusion compounds are compared with those observed for the furaltadone base and moxnidazole hydrochloride. The latter is a closely related species to furaltadone hydrochloride, with an N-methylnitroimidazole ring instead of the nitrofuran moiety. However, the observed configuration of moxnidazole and, consequently, the relative orientation of its polar groups are different in order to avoid intramolecular steric hindrance. As an apparent result, no clathrate-type channels are formed when a hydrate of moxnidazole hydrochloride crystallizes from water. The solvent-free structure of furaltadone is dominated by characteristic dipole-dipole interactions between molecules located across crystallographic centers of symmetry. Remarkably similar interactions of dipolar “dimerization” are present in the compounds containing furaltadone (but not moxnidazole) hydrochloride; we thus suggest that they are significant to the formation of the observed channel inclusion structures. Relative stability of the inclusion compounds is discussed, and molecular geometries of all the involved species are described in detail. Molecules of acetic acid appear in the channel complexes as isolated monomeric species.