Background Flow cytometry has been used in many different settings to, for example, analyse subpopulations of leucocytes in quality control of stem cell grafts and in the diagnosis of lymphoma and leukaemia. In transfusion medicine, it has mainly been utilized for detection and semiquantification of various blood group antigens as a complement to traditional serology, for quality control of blood components and detection of fetomaternal haemorrhage. Today, when flow cytometers are becoming smaller, cheaper and more user friendly and are available in many routine laboratories, the method should be considered as a valuable tool to use in addition to serology and genomic typing.Objectives To give an overview of how flow cytometry can be useful in a transfusion medicine setting as a complement to both traditional serology and molecular testing.Conclusion Flow cytometry has the advantages of a higher sensitivity for some antigens than in traditional serology and the ability to easily distinguish between two or more populations of cells, which makes it a useful tool in many clinical settings, for example in defining chimeras and in detection of fetomaternal bleeding. The combination of molecular testing and the detection of surface antigens by flow cytometry are found useful. When resolving clinically relevant ABO discrepancies we have found the combination of genetic testing and semiquantification of ABO antigens by flow cytometry very helpful. Taken together flow cytometry is a handy tool in clinical routine analysis as well as in research focusing on transfusion medicine.