A major challenge in cancer treatment is the quantification of biomarkers associated with a specific cancer type. Important biomarkers are the circulating tumor cells (CTCs) detached from the main cancer and circulating in the blood. CTCs are very rare and their identification is still an issue. Although CTCs quantification can be estimated by using fluorescent markers, all the fluorescence techniques are strongly limited by the number of emissions (therefore markers) that can be discriminated with one exciting line, by their bleaching characteristics, and by the intrinsic autofluorescence of biological samples. An emerging technique that can overcome these limitations is Surface Enhanced Raman Scattering (SERS). Signals of vibrational origin with intensity similar to those of fluorescence, but narrower bandwidths, can be easily discriminated even by exciting with a single laser line. We recently showed the benefit of this method with cells fixed on a surface. However, this approach is too demanding to be applied in clinical routine. To effectively increase the throughput of the SERS analysis, microfluidics represents a promising tool. We report two different hydrodynamic strategies, based on device geometry and liquids viscosity, to successfully combine a microfluidic design with SERS.