The retention characteristics and separation selectivity of a novel latex nanoparticle (NP) pseudostationary phase (PSP) for electrokinetic chromatography have been characterized. The anionic NPs have very low or no affinity for cationic solutes, but show significant interactions and retention based on hydrophobic interactions. Retention factors of alkyl-phenyl ketones increase linearly with the concentration of the NPs and have zero or near zero y-intercepts as expected for electrokinetic chromatography with non-micellar PSPs. The retention factors of these solutes and representative pharmaceuticals decrease logarithmically with increases in the concentration of ACN in the background electrolyte, as expected for reversed-phase retention. Linear solvation energy relationship analysis indicates that the NPs are less cohesive than would be expected for polymeric PSPs with similar structure but that the overall separation selectivity can be expected to be similar to polymer PSPs with similar backbone chemistry. The results indicate that the hydrophobic core of the NPs is non-cohesive and is highly accessible to solutes, whereas the ionic head groups are not as accessible and do not contribute substantially to retention or selectivity.