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Composite microsystems that incorporate microelectromechanical and microelectrofluidic devices are emerging as the next generation of system-on-a-chip (SOC). We present a performance comparison between two types of microelectrofluidic systems (MEFS): continuous-flow systems and droplet-based systems. The comparison is based on a specific microelectrofluidic application-a polymerase chain reaction (PCR) system. The behavioral modeling, simulation, and performance evaluation are based on a SystemC design environment. The performance comparison includes the system throughput, system-correction capacity, system-processing capacity, and system-design complexity. By using our system-performance evaluation environment, we demonstrated that the droplet-based MEFS provides higher performance, as well as lower design and integration complexity.