Real-time quantitative PCR (qPCR) is a preferred platform for high throughput gene expression profiling, where large numbers of samples are characterized for hundreds of expression markers. Technically, the qPCR measurements are performed in the same way as when classical qPCR is used to analyze only a few targets per sample, but the higher throughput introduces additional sources of potential confounding variation that must be controlled for. In this presentation, Dr Kubista describes how high throughput qPCR profiling studies are designed. He covers assay optimization and validation, sample quality testing, and how to merge multi-plate measurements into a common analysis. Dr Kubista also discusses how to cost-effectively measure and compensate for background due to genomic DNA.