Nowadays in human and animal andrology flow cytometry is recognized as a robust tool for the evaluation of sperm quality and function. However, in this particular field, this technique has not reached the sophistication of other areas of biology and medicine. In recent years more sophisticated flow cytometers are being introduced in andrology laboratories, and the number of tests that can be potentially used in the evaluation of the sperm physiology has increased accordingly. In this review recent advances in the evaluation of sperm will be discussed; representing new techniques in flow cytometry, many of them able to measure simultaneously, in a single test, different degrees of damage in different sperm regions and/or changes in functionality.