The count of colony-forming units (CFUs) in a microbial sample estimates the number of viable cells in that sample, defined as the number of cells that are alive and will divide to produce more cells. The estimate is made by diluting and culturing the sample, then counting the resulting colonies. Since colonies may be started by clumps of cells, the CFU count is usually an underestimate of the number of viable cells. Rather, it is the minimum number of viable cells that must have been present to start the observed colonies.

Probiotic supplements containing live bacteria or yeasts usually list the number of CFUs in each dose. Note that this count is made before the microbes encounter the digestive system. Individual strains have different abilities to survive, and probiotics may be packaged in ways that enhance survivability.