We explore the use of preparative size-exclusion chromatography (SEC) and high-performance liquid chromatography (HPLC) to purify quantum dots (QDs) after surface modification. In one example, in which Bio-Beads (S-X1) were used as the packing material for the preparative SEC column, CdSe QDs treated with a functional coumarin dye could be separated from the excess free dye by using tetrahydrofuran (THF) as the mobile phase. This column was unable to separate polymer-coated QDs from free polymer (M approximately 8000) because of the relatively low cutoff mass of the column. Here a preparative HPLC column packed with TOYOPEARL gel allowed the effective separation of polymer-bound QDs from the excess free polymer by using N-methyl-2-pyrrolidinone (NMP) as the mobile phase. When other solvents such as absolute ethanol, acetonitrile, THF, and THF-triethylamine mixtures were used as the eluent, QDs stuck to the column. While NMP was an effective medium to remove excess free polymer from the QDs, it was difficult to transfer the purified QDs to more volatile solvents and maintain colloidal stability.