We have developed a method for high resolution, high magnification immunofluorescence-based screening in a multi-well format, using a recently introduced 96-well plate specifically developed for fluorescence microscopy. We report here on the use of these plates to screen hybridoma supernatants for reactivity with specific subcellular compartments of the protozoan parasite Toxoplasma gondii. This has proven to be a powerful screening strategy, particularly when combined with high-throughput immunoblotting, and has enabled us to generate nine different monoclonal antibodies (MAbs) against either the periphery or structures within the apical end of T. gondii. The availability of a disposable, inexpensive, 96-well plate with optical properties suitable for high magnification imaging could lead to applications in a variety of fluorescence-based screening protocols.