Abstract: A massively parallel electrophoresis system comprised of capillaries, with means for parallel imaging of the capillary ends. The capillaries are aligned with parallel longitudinal axes and a set of ends that are substantially coplanar. The electrophoresis system has a source of excitation radiation for illuminating the ends while an imaging optical arrangement places substantially coplanar loci, one per capillary, within a focal region of the imaging optical arrangement. A detector module receives electromagnetic radiation that is emitted by fluorophores within the capillaries upon excitation by the excitation radiation and transmitted to the detector module by way of the imaging optical arrangement.