Gold nanoparticles (AuNPs) and poly(ethylene glycol) (PEG) are known to be safe, biocompatible materials. In this study, AuNPs were conjugated with PEG ligands, and the suspensions of AuNPs with and without free PEG ligands were characterized using UV-visible spectroscopy, hydrodynamic size measurement, and time-of-flight SIMS (ToF-SIMS) imaging analysis. The two AuNPs solutions were each dropped onto a hydrophilic surface (bare Si wafer) and a hydrophobic surface (a plasma-polymerized cyclohexane-coated Si wafer), then dried to produce self-aggregated micropatterns, from which ToF-SIMS images were obtained. From these ToF-SIMS images, we calculated the Pearson product–moment correlation coefficient (PMCC) of the AuNPs and PEG intensities to quantitatively measure the coexistence of both materials in the solution. Good coexistence between AuNPs and PEG ligands was obtained only from the sample film prepared by dropping the suspension of PEG-conjugated AuNPs without free ligands onto a hydrophobic surface. The degrees of coexistence (i.e. PMCC value) seem to correlate with the amount of free PEG ligands in suspension to affect the stability of organic conjugated nanoparticles in solution. In addition, it was found that minimal interaction between the conjugated ligands and the substrate used for the sample film preparation led to an optimum PMCC statistical analysis. Our results lead us to believe that this new approach could simplify the method by which to quantitatively study the degrees of coexistence between nanoparticles and ligands, the amount of free ligands, and the stability of ligand-conjugated nanoparticles in suspension. Copyright © 2012 John Wiley & Sons, Ltd.