Recent studies have shown that membrane-water partition coefficients of organic chemicals can be used to predict bioaccumulation and type I narcosis toxicity more accurately than the traditional K(OW)-based approach. In this paper, we demonstrate how comprehensive two-dimensional gas chromatography (GC × GC) can be used to estimate such membrane-water partition coefficients (K(PLW)s), focusing in particular on phosphatidyl choline based lipids. This method performed well for a set of 38 compounds, including polycyclic aromatic hydrocarbons, polychlorinated benzenes and biphenyls, and substituted benzenes including some phenols and anilines. The average difference between the estimated and the measured log K(PLW) values of 0.47 log units is smaller than in the case of a log K(OW) correlation approach but larger than seen using a polyparameter linear free energy relationship based approach. However, the GC × GC based method presents the advantage that it can be applied to mixtures of chemicals that are not completely identified, such as petroleum hydrocarbon mixtures. At the same time, our application of the GC × GC method suffered larger errors when applied to certain hydrogen bonding compounds due to the inability of the GC × GC capillary columns phases that we used to interact with analytes via hydrogen bond donation/electron acceptance.