As the biopharmaceutical and clinical diagnostics industries are faced with increasing numbers of assays as well as a higher level of scrutiny on quality, automation is becoming more prevalent than ever before. Automation operating at its best can increase throughput by providing around-the-clock testing and improve repeatability by performing tedious yet critical tasks. However, there are several challenges in automating an assay workflow. Some challenges affect operational efficiency, while others affect assay performance. This tutorial will focus on assay performance by examining contributions to assay variability and methods to reduce the effects. Specifically, we will explore manual to automation transfer and automated liquid handling validation. Example assay workflows that for clinical samples and genomic tests like RT-PCR or NGS will be discussed.