With the increase in demand for high-speed cell sorting of viable infectious and now therapeutic cell samples, safety concerns for the protection of flow cytometer operators have increased. This chapter describes a quick, sensitive, and reproducible procedure to assure sample containment before sorting these samples. This procedure includes aerosol containment, physical barriers, environmental controls, and personal protection. An aerosol management system produces a negative pressure within the sort chamber where aerosols are vacuumed directly into a HEPA filter. Physical barriers include the manufacturer's standard plastic shield and panels. The flow cytometer is contained in a BSL-3 laboratory for maximum environmental control and the operator is protected using a respiratory system. Containment is measured using highly fluorescent Glo-Germ particles under the same conditions as the cell sort but with the sorter adjusted to produce large amounts of aerosols. These aerosols are collected by a vacuum air sampling system for 10 min in three locations onto a glass slide and examined microscopically. With this system in place, aerosol containment can be measured quickly and efficiently, therefore reducing the risk to the operator when sorting viable infectious cells.