The biocompatible semiconductor quantum dots (QDs) have unique photophysical properties, which provide important advantages over organic dyes and lanthanide probes in fluorescence labeling applications. In this work, multicolor quantum QD-encoded microspheres have been prepared via the layer-by-layer (LbL) assembly approach. Polystyrene microspheres of 3mum diameter were used as templates for the deposition of different sized CdTe QDs/polyelectrolyte multilayers via electrostatic interactions. Two kinds of biofuntional multicolor microspheres with two different antibodies, anti-human IgG and anti-rabbit IgG were prepared. Human IgG and rabbit IgG can be detected as target antigens in the multiplexed fluoroimmunoassays. Furthermore, a novel microfluidic on-chip device was developed to detect two kinds of antigen-conjugated multicolor QD-encoded microspheres; the microspheres can be distinguished from each other based on their fluorescence signals.