Sepsis is a major killer of man and infected soldiers in the field because the microbial load in blood overcomes even the most powerful existing antibiotic therapies and eventually leads to multi-systems failure. This is a particularly significant problem in premature infants and immuno-compromised patients with fungal infections because use of antifungal therapies is limited by their high toxicity. Development of an extracorporeal blood cleansing device that can be inserted into peripheral blood vessels and rapidly clear the blood of pathogens without removing normal blood cells, proteins, fluids or electrolytes could help remedy this problem, especially when used with low-dosage antifungal agents. We have developed a prototype microfluidic-micromagnetic blood cleansing device that rapidly clears relevant fungal pathogens (e.g. Candida albicans) from flowing human whole blood with high efficiency and throughput. The cell separation device is composed of a multiplexed array of linked microfluidic channels microfabricated from poly-dimethylsiloxane (PDMS). Magnetic opsonins were made using 1-μm superparamagnetic microbeads coated with pathogen-specific antibodies. Using a prototype of the microfluidic blood cleansing device we have selectively remove nearly 80% of living fungal pathogens from a continuously flowing stream of heparinized human whole blood (20 ml/hr/device) in a single pass. We have since further enhanced the volumetric throughput of our devices through multiplexing and optimization of our microfluidic channel designs. Using our high-efficiency and high-throughput microfluidic cell separation devices, we are able to selectively remove fungi and reduce the time necessary to decrease the pathogen load of a continuously flowing stream of contaminated human whole blood.