Flow cytometers having an enclosed particle sorting module are provided. Aspects of the flow cytometers include, in addition to the enclosed particle sorting modules, a sample input module fluidically coupled to an inlet of the enclosed particle sorting module, a waste reservoir fluidically coupled to first outlet of the enclosed particle sorting module and a first sorted particle collection system fluidically coupled to a second outlet of the enclosed particle sorting module. Flow cytometers as described herein are configured to control aerosol content in the enclosed particle sorting modules, including the sort chambers of such modules. Also provided are methods of using the flow cytometers, as well as kits that include one or more components of the flow cytometers are consumables for use therewith.