A microfluidic device for random fragmentation of DNA or RNA based on the application of a hydrodynamic shear force to these biomolecules is presented. Different from conventional fragmentation instruments, the microchip-based implementation allows molecules to be repetitively sheared and broken during a single run through the device. It therefore requires comparatively few external components and has a low dead volume in the order of 0.5 μL. 48 kbp λDNA could be fragmented down to an average size of 4 kbp at a flow rate of 1 mL/min.