Hexachlorocyclohexane (HCH, C6Cl6H6) is a persistent chemical that can be found around the globe in various environmental compartments. Much research has been conducted on its environmental fate, but there remains a controversy regarding the basic physicochemical properties of its isomers. We have therefore measured additional partition data for alpha-, beta-, and gamma-HCH using chromatographic measurements to resolve this existing controversy. The results reveal a distinctly different partition behavior of beta-HCH compared to alpha- and gamma-HCH. The ability of various models to predict this partition behavior from molecular structure was investigated. SPARC and EPI-suite failed to predict any isomeric differences. COSMOtherm, a quantum chemical software, correctly predicted the qualitative differences between the isomers, but in some cases, the predicted absolute values differed by more than 1 order of magnitude. In addition, the COSMOtherm software was used to predict partition data for the three isomers of the flame retardant hexabromocyclododecane (HBCD) revealing results similar to HCH.