A critical need exists for advanced technologies that enable genomic-based DNA analysis to be performed with significantly higher throughput and at a significantly lower cost than is attainable with current hardware. Miniaturized polymerase chain reaction systems offer an attractive platform to address these needs, combining the ability to perform rapid thermocycling with a portable device format that can be inexpensively mass produced. We review recent efforts aimed at developing these next-generation systems and discuss some of the practical considerations involved in adapting this technology for routine laboratory use.