Abstract Modern drug discovery and genomic analysis depend on rapid analysis of large numbers of samples in parallel. The applicability of microfluidic devices in this field needs low cost devices, which can be fabricated in mass production. In close collaboration, Greiner Bio-One and Forschungszentrum Karlsruhe have developed a single-use plastic microfluidic capillary electrophoresis (CE) array in the standardized microplate footprint. Feasibility studies have shown that hot embossing with a mechanical micromachined molding tool is the appropriate technology for low cost mass fabrication. A subsequent sealing of the microchannels allows sub-microliter sample volumes in 96-channel multiplexed microstructures.