Lab-on-chips (LOCs) are microsystems capable of manipulating small (micro to nanoliters) amounts of fluids in microfluidic channels with dimensions of tens to hundreds of micrometers: they have a huge application potential in many diverse fields, ranging from basic science (genomics and proteomics), to chemical synthesis and drug development, point-of-care medical analysis and environmental monitoring. Polymers are rapidly emerging as the material of choice for LOC production, due to the low substrate cost and ease of processing. Notwithstanding their potential, LOC commercial exploitation has been slow so far. Two breakthroughs that could promote LOC diffusion are: (i) a microfabrication technology with low-cost rapid prototyping capabilities; (ii) an integrated on-chip optical detection system.In this project we propose the use of femtosecond lasers as a novel highly flexible microfabrication platform for polymeric LOCs with integrated optical detection, for the realization of low-cost and truly portable biophotonic microsystems. Femtosecond laser processing is a direct, maskless fabrication technique enabling spatially selective three-dimensional material modification. It will be employed in different steps of the LOC production cycle: (i) rapid prototyping of the microfluidic chip using laser ablation or two-photon polymerization; (ii) direct fabrication of optical waveguides and integrated photonic components on the LOC for in situ optical sensing; (iii) master tool fabrication for mass production by replication techniques.The laser fabrication technology will enable to implement a variety of microfluidic LOCs with integrated photonic functionalities. In this project we concentrate on two prototypical applications in the fields of food quality and environmental sensing: LOCs for detection of mycotoxins in animal feeds and LOCs for water screening to detect bacteria and heavy ions contamination.