A porous silicon (PSi) based microarray has been integrated with a microfluidic system, as a proof of concept device for the optical monitoring of selective label-free DNA-DNA interaction. A 4 × 4 square matrix of PSi one dimensional photonic crystals, each one of 200 μm diameter and spaced by 600 μm, has been sealed by a polydimethylsiloxane (PDMS) channels circuit. The PSi optical microarray elements have been functionalized by DNA single strands after sealing: the microfluidic circuit allows to reduce significantly the biologicals and chemicals consumption, and also the incubation time with respect to a not integrated device. 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 DNA probe and target has been monitored by spectroscopic reflectometry for each PSi element in the microchannels.