Assays employed in HTS and lead optimization projects in drug discovery should be rigorously validated both for biological and pharmacological relevance, as well as for robustness of assay performance. This chapter addresses the essential statistical concepts and tools needed in assay performance validation developed in the pharmaceutical industry, specifically for higher throughput assays run exclusively in 96-, 384- and 1536-well formats using highly automated liquid handling and signal detection systems. In this context, it is assumed that the biological and pharmacological validation of the assay system has already been established, and the high through put performance characteristics requires validation. This is an essential chapter for these who design and implement HTS and lead optimization assays to support SAR projects in pre-clinical drug discovery.