High-throughput screening (HTS) can efficiently assay multiple discrete biological reactions using multi-well microplates. The choice of microplate is a crucial yet often overlooked technical decision in HTS and quantitative biology. This chapter reviews key criteria for microplate selection, including: well number, well volume and shape, microplate color, surface treatments/coatings, and considerations for specialized applications such as high-content screening. This chapter then provides important technical advice for microplate handling including mixing, dispensing, incubation, and centrifugation. Special topics are discussed, including microplate surface properties, plate washing, well-to-well contamination, microplate positional effects, well-to-well and inter-lot variability, and troubleshooting. This information and best practices derived from academic, government, and industry screening centers, as well as microplate vendors, should accelerate assay development and enhance assay quality.