This paper reports on the first demonstration of polymeric microfluidic cantilever sensors. Microcantilever sensors, magnetic beads, and microfluidic technology have been combined to create a polymer based biosensor. Using cheap materials like polyimide, a simple fabrication method has been developed to produce cantilevers with an embedded microfluidic channel. The advantage of this approach is that the addition of a microfluidic channel enables the analysis of smaller volumes and increases the capture efficiency in applications detecting rare analytes. As a proof of principle the system has been applied for the detection of the waterborne protozoan parasite Cryptosporidium, achieving sensitivity comparable to QCM, whereas a previous set-up without the microfluidic channel was unable to detect the parasite.