In recent years, the use of polymer materials in the field of microfluidic systems and so-called ’lab-on-a-chip’ systems has increased. Silicon, the material traditionally used for the fabrication of such systems, is not compatible with for instance blood or harsh chemicals, while many polymers have the desired properties. A number of standard polymers like poly(methyl methacrylate) and polydimethylsiloxane have been investigated, but also new polymer types with e.g. superior optical or chemical properties have emerged in microfluidic research. The lab-on-a-chip systems integrate fluidic handling and measurement on a single chip, and both optical and electronical components can be embedded. For polymer microsystems, integration of optical waveguides can be achieved by structuring polymers with different refractive indices. This thesis treats aspects of prototyping and fabrication of microfluidic systems in polymers, mainly in the cyclic olefin copolymer Topas. This relatively new polymer is resistant to a large number of chemicals and to strong acids, making it suited for microfluidic systems used e.g. for long term waste water monitoring. The high refractive index and other good optical properties makes it suited for integrated optics in microfluidic systems. Also, the engineerable glass transition temperature is an advantage, when making single-polymer systems. During the project existing fabrication methods have been adapted or improved for use with Topas, so that a number of tools for rapid prototyping of this polymer is now available. These tools include: • Micro milling of fluidic channels and optical waveguides with dimensions down to 25 μm. • Spin coating of polymer layers on polymer substrates with a thickness from 100 nm to 20 μm. The spin coat layers act as a glue for joining the substrate, optical layers and the lid in the microfluidic systems. • Thermal bonding of polymer structures, including roll lamination of foil onto substrates. • Laser bonding of two polymer layers, including transparent on black, and transparent on transparent with a particle doped spin coating. • Thermal treatment of waveguides to improve the surface roughness and lower the propagation loss. The fabrication methods have been characterised, and have been optimised to minimise parameters like fabrication time, surface roughness and interface bonding strength. Using these fabrication methods, microfluidic structures have been produced. Also, optical waveguides have been produced, exploiting the difference in refractive index of different Topas grades. Finally, optical absorption measurements have been carried out in a microfluidic system with integrated waveguides. A demonstrator capable of distinguishing between liquids with different refractive index – in our case water and a saturated solution of sugar in water – was produced using all of the techniques developed during the studies, and drawing from the knowledge about waveguides in Topas obtained in the experiments mentioned above. Finally, in a collaboration with IMTEK in Freiburg, Germany, an optical detection principle was developed. Using the principle of total internal reflection of a laser beam incident on a fluidic channel, detection of air bubbles is possible. The principle was used on a rotating platform as well as on non-moving systems.