An instrument is disclosed for fluorescence assays which is capable of reading many independent samples at the same time. This instrument provides enhanced throughput relative to single-sample instruments, and is well-suited to use in general fluorescence, time-resolved fluorescence, multi-band fluorescence, fluorescence resonance energy transfer (FRET), and fluorescence polarization. This invention is beneficial in applications such as high-throughput drug screening, and automated clinical testing. Also disclosed are means and methods for a fluorescence polarization measurement which is highly sensitive, inherently self-calibrated, and unaffected by lamp flicker or photobleaching. This fluorescence polarization invention can be practiced on a variety of fluorescence instruments, including prior-art equipment such as microscopes and multi-well plate readers.