Cell mechanical phenotype, or ‘mechanotype’, is emerging as a valuable biomarker for the physiological or diseased state of cells. Established techniques such as micropipette aspiration and atomic force microscopy provide quantitative insights into the viscoelastic properties of cells. However, to acquire data across a larger number of samples within a reasonable timescale requires higher throughput measurements. The recent development of fluidic-based mechanotyping methods enable data acquisition at rates of up to 2000 cells/second1,2, but require image-based analysis that hinders simultaneous measurements across an array of cell samples. Here we present a protocol for measuring the ability of cells to filter through micron-scale pores using a simple and scalable technique called parallel microfiltration (PMF). Cell filtration depends on the ability of cells to deform through micron-scale pores, and can thus provide a measure of cell deformability. The PMF method can be used for screening of multiple cell samples in parallel based on cell filtration. The entire protocol, from preparation of cell suspensions to readout of filtration, can be completed within an hour. Here we demonstrate the applicability of PMF to measure human promyelocytic leukemia (HL-60) cells, as well as human ovarian (OVCAR3 and OVCAR5) and breast cancer (MDA-MB-231) cells. The method can easily be adapted for use with other mammalian cell types.