Multiple probes/primers expand the capability of single-probe real-time PCR. Multiplex real-time PCR uses multiple probe-based assays, in which each assay have a specific probe labeled with a unique fluorescent dye, resulting in different observed colors for each assay. Real-time PCR instruments can discriminate between the fluorescence generated from different dyes. Different probes/primers are labeled with different dyes that each have unique emission spectra. By combining the encoded microbeads and real-time PCR amplification, it is possible to increase the multiplexity of PCR experiments to a very large number, such as 128 with 7 digit or 4,096 with 12-digit barcode. Oligonucleotide probes/primers labeled with encoded microbeads offer the ability to monitor the reaction kinetics of each probe which is tagged with barcoded beads.