Collection systems for flow cytometrically sorted samples are provided. Aspects of the collection systems include: a collection container having a sort tube configured to be in droplet receiving relationship with a sort block of a flow cytometer; and a sample output operatively coupling a cell collection location of the collection container to a mating connection for a receiving container, such as an evacuated receiving container. Also provided are methods using the collection systems, as well as assemblies and kits including components of the systems.