Microplates containing an 8 x 12 array of 96-wells are the most prevalent format for screening compound libraries in high-throughput applications today. These plates are suitable for use in a wide variety of homogeneous and heterogeneous assays to measure binding interactions, enzyme activity and cell proliferation. Assays widely performed in microplates include immunoassays, scintillation counting methods and cell proliferation assays; highly sensitive fluorescence-based assays have recently been introduced for microplate formats. Instrumentation for plate handling and reading assay data in the 96-well format is currently available. Future directions involve assay miniaturization in high density plates and automating the entire screening process.