Robust, user-friendly and state-of-the-art fluorescence activated cell sorter (FACS) which allows isolation of individual cells and pathogens from complex cell mixtures derived e.g. from body fluids and tissues based on different cell characteristics (size, granularity and fluorescence). Isolated cells can be characterized in molecular detail, either directly or upon further cultivation. As such, FACS represents an essential tool in a plethora of life science research domains. Since FACS involves live cells and pathogens, it requires on-site access by users to avoid transport-associated impaired cell viability or biosafety risks. The FACS is easy-to-use decreasing the threshold for inexperienced research groups to implement FACS technology in their research lines. Furthermore, the equipment is state-of-the-art with regard to the applications needed, e.g. plate sorting for possible single cell omics, temperature-controlled sample loader and sort collection recipients, covering at least >95% of the types of sorting procedures at the Faculty of Veterinary Medicine. The cell sorter is housed at the campus of the Faculty of Veterinary Medicine in a room dedicated to cell sorting within a BSL2 laboratory. This room is equipped with climate control and access to external air pressure to meet the needs to operate a cell sorter, e.g. a stable temperature to avoid excessive heat, which might disturb the sorting process, and noise reduction, respectively. This equipment is of invaluable use for veterinary research at Ghent University, exemplified by a variety of projects the equipment is involved in.