An assay unit for carrying-out fluorescence-detected assays having a microfluidic chip with a microfluidic system to convey a sample or analyte solution through one or more microfluidic channels arranged on the chip, and a photonic system with two or more rectangular waveguide structures. The microfluidic channels and the waveguide structures cross each other at a detection site. In an assay area, where a certain microfluidic channel and a certain waveguide structure cross each other, one or more lateral surfaces of the core of the waveguide structure at least partially face an inner volume of the microfluidic channel, such that an evanescent field of light guided within the waveguide structure overlaps with a certain part of the inner volume of the microfluidic channel.