Comprehensive high-performance liquid chromatography (HPLC) analyses were performed on poly(amidoamine) (PAMAM) dendrimer based multifunctional devices. The nanometer-size devices were synthesized by conjugating partially acetylated (Ac) poly(amidoamine) dendrimers of generation 5 (G5) with fluorescein isothiocyanate (FITC), folic acid (FA) and methotrexate (MTX). The devices are intended for targeted intracellular drug delivery to tumor cells through the folate receptor. Methods were developed for detection and separation of various surface functionalized dendrimer conjugates and small molecules (FITC, FA, MTX) using a common gradient. Results indicate that the HPLC technique can be used as a quality control tool for determining purity of the G5 carrier, its acetylated form, and mono-, bi- and tri-functional nanodevices. More importantly, the chromatograms of these novel nanodevices, reported for the first time, provide information on critical properties such as polydispersity, surface heterogeneity and solubility. The benchmark data can be used to optimize the physicochemical properties of the conjugates to improve drug delivery to cancer cells.