A novel microfluidic sensing device based on waveguide cavity filters is proposed for the characterisation, detection of cells in solution and chemical substances in micro-litre volumes. The sensor consists of a micromachined microfluidic channel within a waveguide-based resonator localised increased near-fields and could potentially be designed for different frequency regimes to improve the sensitivity. The present sensor has been proposed for fabrication in different manufacturing platforms and an initial prototype with a 100µm micromachined channel that is embedded within an X-band E-plane waveguide has been fabricated and tested. The design methodology for the microfluidic channel and the E-plane filter is also presented. © 2009 IOP Publishing Ltd.