Significant advances in treatment have enabled previously infertile males to achieve fatherhood, when only a few years ago they would have had no chance of biological paternity. In contrast to the overall success of assisted reproduction, the aetiology of male-factor infertility is poorly understood. Recent studies have shown, however, that a significant proportion of men with severe infertility have microdeletions of the Y chromosome. Furthermore, reports have shown that male infants conceived through assisted reproductive techniques have inherited the same Y-chromosome microdeletion as their fathers. It has thus become important to screen men who are at risk of Y-chromosome microdeletions, as this will determine if counselling is needed prior to starting infertility treatment. This review examines the significance and limitations of the current understanding of Y-chromosome microdeletions in male infertility.