Flow cytometry is a technique in which sub-populations of cells can be analysed and separated according to the staining pattern seen with various fluorescent markers. This review describes some of the ways in which flow cytometry can be applied to the investigation of sperm populations, either as a means of quality control of semen or to examine the characteristics of different sub-populations of sperm within an ejaculate. These methods can replace or augment existing subjective assessments of semen characteristics. Using this technique it is possible to produce aliquots of sexed sperm for insemination or for in vitro fertilisation. An objective assessment can be made of the effects of environmental stress on male physiology by monitoring changes in semen quality.