A porous silicon (PSi) based microarray has been integrated with a microfluidic system based on polydimethylsiloxane (PDMS) channels circuit, as a proof of concept device for the optical monitoring of selective label-free DNA-DNA interaction. Theoretical calculations, based on finite element method, taking into account molecular interactions, are in good agreement with the experimental results, and the developed numerical model can be used for device optimization. The functionalization process and the interaction between probe and target DNA has been monitored by spectroscopic reflectometry for each PSi element in the microchannels.