BACKGROUNDApplications of fluorescence-activated cell sorting (FACS) are ideally performed under aseptic conditions so that isolated cells can be successfully cultured, transplanted, or processed for the isolation of protein and nucleic acids. However, modern "off-the shelf" flow cytometers are suboptimally designed for these purposes because nonsterile instrument hardware components directly contact sample-harboring fluids, compromising their sterility.METHODSWe have described the design and modular modification of a cytometer with a sterile and disposable FACS fluid handling system that meets requirements of high-speed FACS and good manufacturing practice. This system was tested for functionality and its ability to maintain a clean and sterile fluid environment.RESULTSOur data have shown that this new fluidic subsystem completely replicated the intended function of the manufacturer's standard fluid handling system, and isolates the fluid from contaminants such as bacteria and fungus, endotoxins, mycoplasma, and helicobacter.CONCLUSIONSFACS has emerged as a powerful tool used to study and manipulate stem cells. However, if stem cell discoveries are to be fully utilized in clinical transplant medicine, aseptic instrument configurations must be developed. For this purpose, we have designed a disposable sterile fluid handling system.