Editor-In-Chief: C. Michael Gibson, M.S., M.D. 
In microbiology, colony-forming unit (CFU) is a measure of viable bacterial numbers. Unlike in direct microscopic counts where all cells, dead and living, are counted, CFU measures viable cells. By convenience the results are given as cfu/mL (colony-forming units per milliliter).
The theory behind the technique of CFU establish that a single bacteria can grow and become a colony, via binary fission. These colony are clearly different between each other, both microscopical and macroscopical. However, some bacteria do not separate completely during the sample preparation process (Staphylococcus, Streptococcus) and the results of the count will be below the number of individual cells using direct methods.
This technique allows the user to know how many CFU are per mL in the sample. Therefore, it allows knowing which is the microbiological load and the magnitude of the infection in humans and animals, or the degree of contamination in samples of water, vegetables, soil or fruits and in industrial products and the equipment.
Irradiated mice can have their immune systems reconstituted by the injection of bone marrow cells from a non irradiated animal. The injected cells form colonies in the spleen (hence s), each colony representing the progeny of a pluripotent stem cell. Operationally, therefore, the number of colony-forming units is a measure of the number of stem cells.