The growing number of standards commercially available in the field of flow cytometry makes it difficult to know which standards to use to obtain a desired level of quality assurance. A classification system of fluorescence standards has been developed on the basis of their physical characteristics. In turn, these physical characteristics determine the ability of the specific standards to perform selected functions, such as alignment, target referencing, compensation, and calibration. Knowing the properties and limitations of specific standards will help flow cytometer users to select the appropriate standard for the application that they will be performing, especially in regard to intra- and interlaboratory quality assurance. Common protocols used in conjunction with specific classifications of reference standards can provide unified analysis regions or window of analysis across different instruments and/or laboratories. In addition, specific classifications of calibration standards can help select those standards that will provide independent and direct comparison of instrument performance parameters, especially in studies involving multiple laboratories. Knowledge and understanding of the classification system can guide flow cytometer users in more efficient and accurate instrument setup and quality control when conducting research, as well as clinical applications.