Carcinoma of prostate (CaP) is the second most frequent malignant tumour occurring in men in Europe. Currently there is discussed a wide range of potential CaP markers. One of them - non/protein amino acid sarcosine, also known as N-methylglycine was chosen as a challenge for the development of microfluidic system with isolation by modified paramagnetic microparticles (PMPs). Therefore, the aim of this study was to design a low-cost, simple and rapid microfluidic system based on sarcosine isolation with modified paramagnetic microparticles and subsequent analysis on the ion-exchange liquid chromatography. We modified Dowex microparticles with Fe2O3 nanoparticles. Our paramagnetic microparticles were able to establish the binding with sarcosine. Moreover, we designed microfluidic device for sarcosine determination. Analysis of samples was carried out with limit of detection of 1 μM of a sarcosine that is sufficient because it is similar to concentrations of a sarcosine observed in the CaP patients.