High-throughput, quantitative and rapid microfluidic-based separations has been a long-sought goal for applications in proteomics, genomics, biomarker discovery and clinical diagnostics. Using droplet-interfaced microchip electrophoresis (MCE) techniques, we have developed a novel parallel MCE platform, based on the concept of combining the Slipchip principle with a newly developed 'Gelchip'. The platform consists of two plastic plates, with droplet wells on one plate and separation channels with preloaded/cured gel in the other. A single relative movement of one plate enables generation and then loading of multiple sample droplets in parallel into the separation channels, allowing electrophoretic separation of biomolecules in the droplets in parallel and with high-throughput. As proof of concept, we demonstrated the separation of 30 sub-nanolitre sample droplets containing fluorescent dyes or DNA fragments.