Polydisperse samples of Au nanoparticles protected with monolayers of hexanethiolate ligands (C6 MPCs) and with mixed monolayers of hexanethiolate and mercaptoundecanoic acid (C6/MUA MPCs) have been chromatographically separated using C8 120-A columns and acetone/ toluene mobile phase. The spectral details of eluted peaks and of quantized double-layer charging features in the differential pulse voltammetry of collected fractions were used to show that the elution orders of C6 MPC mixtures and of C6/MUA MPC mixtures were different. For C6 MPCs, the smallest MPCs were eluted first, whereas the smallest C6/MUA MPCs were eluted last. The reversal of order of elution was rationalized in terms of intermolecular interactions with the stationary phase, dominant for the C6 MPC, being suppressed by the heightened polarity of the monolayer surface of the C6/MUA MPCs, making a size exclusion mechanism dominant. The range of apparent core diameters of the separated nanoparticles was 1.3-2 nm.