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Advanced assisted reproductive technologies such as in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) are established treatment for severe male-factor infertility. The risk of transmitting existing genetic abnormalities to offspring through assisted reproduction has been a particular concern in male infertility cases due to Y-chromosome microdeletion, congenital bilateral absence of the vas deferens and Klinefelter’s syndrome, because these conditions generally required ICSI to achieve pregnancy. In addition, earlier studies raised the concerns of increased spontaneous abortion rate and chromosomal abnormalities with IVF and ICSI. Recently, well designed, large scale, population based studies concluded that assisted reproductive technology accounts for a more than a two-fold increase in the risk of low birth weight and major birth defects. Taken together, the bulk of the literature on the genetic risks of assisted reproduction highlights the importance of adequate pretreatment genetic evaluation and counselling. Furthermore, it is important to have proper infertility evaluation to identify and treat reversible causes of male-factor infertility that would allow couples to conceive naturally or opt for less invasive assisted reproductive technology.