Micro-total-analysis-systems and lab-on-chip are more than promises in lot of social interest applications such as clinical diagnostic or environmental monitoring. There is an increasing demand of new and customized devices with better performances to be used in very specific applications. Nanostructured Porous silicon is a functional material and a versatile platform for the fabrication of integrated optical microsystems to be used in biochemical analysis. Our research activity is focused on the design, the fabrication and the characterization of several photonic porous silicon based structures, which are used in the sensing of specific molecular interactions. To integrate the porous silicon based optical transducer in biochip devices we have modified standard micromachining processes, such as anodic bonding and photo-patterning, in order to make them consistent to the utilization of biological probes.