The changes in farming practices towards bio-production, globalization of food market, global climate change and also the way of food processing facilitate the risks of widespread disseminations of foodborne diseases, including the pathogens of protozoa and multicellular parasites such as Toxoplasma gondii, Trichinella spiralis or Taenia saginata. These facts consequently induce the need of improvement of the diagnostic tools for foodborne agents in the final food products such as meat. In relation to this problematics, our work is focused on development of reliable comprehensive molecular diagnostic method useful for rapid control of meat products on the market. For this purpose, we adopted high sensitive multiplex oligonucleotide ligation- PCR assay - MOL-PCR, representing the novel diagnostic platform based on magnetic microspheres and visualization realized via MAGPIX instrument for qualitative and quantitative readout of signal. This modern approach enables simultaneous direct screen of complex samples potentially containing the DNA originating from number of different parasitic organisms. Up to this date, the specific molecular probes allowing the detection and capturing of targeted DNA from two parasitic worms - Trichinella spiralis (partial sequence of 18S rRNA gene) and Taenia saginata (partial sequence of mitochondrial COX1 gene) were designed. The calibration of the system and optimization of method is in process.