The characterization of quantum dots (QDs) bioconjugates is of great important in biological applications.Our group developed a useful method for characterization of QDs conjugates using capillary electrophoresis coupled with laser induce fluorescence detection (CE-LIF).However, the aggregation of QD-conjugates can not be distinguished by CE-LIF.Fluorescence correlation spectroscopy (FCS) is a single molecule method for characterization of QDs hydrodynamic radii.Herein, we reported the characterization of the QDs conjugates with antibodies using FCS and CE-LIF methods.CdSe/ZnS QDs and two antibodies (AFP 1A6 and AFP 2A5) were used in this study.Figure 1 shows the electrophoregrams of QD-AFP 1A6 and QD-AFP 2A5) conjugates, and this result demonstrates that QDs were successfully conjugated to two antibodies respectively.Figure 2 displays the FCS curves and fluorescent traces of QD-AFP 1A6 and QD-AFP 2A5 conjugates.It was observed that the characteristic diffusion time of QD-AFP2A5 increased dramatically in FCS curves and the certain very strong photon bursting occurred in fluorescent traces.These results illustrated the obvious aggregation of QD-AFP2A5.In conclusion, CE coupled with FCS may be a very useful tool for study of the interaction of QDs and biomolecules in the future.