Poly(dimethylsiloxane) also known as PDMS is used in a wide range of biomedical applications. These range from implants through catheters to soft contact lenses. Therefore, it is understandable that PDMS has been extensively tested for these purposes. In past years, the microfluidics has moved from predominantly silicon and glass structures towards polymers due to their ease of manufacturing and moderate cost. PDMS has gained a lot of attention in various analytical applications. However, the testing of its suitability for such applications has not been as thorough as in the biomedical applications, perhaps relying on the experiments from that field. Microfluidic PDMS structures are more and more popular in various analytical devices. Such devices consume less reagents and can work with lower sample volumes. On the other hand, the surface-to-sample-volume ratio becomes larger. That increases the influence of material properties on the actual measurement. Some of the challenges include adsorption, diffusion, surface roughness, permeability and elasticity of PDMS, which are discussed in this paper.