Gamete nuclear integrity is the most critical parameter to ensure complete and harmonious embryonic development. It is also a major contributor to the health and wellbeing of the progeny. When it comes to nuclear integrity, spermatozoa and oocytes are not equal. The oocyte has DNA repair activities throughout its life while the mature spermatozoa is devoid of it. Therefore, immediately post-fertilization one of the most important tasks of the oocyte is to repair sperm nuclear DNA damage prior to initiating S-phase of the first mitotic division. If there are too many sperm DNA lesions, the repair mechanisms activated in the oocyte may be overwhelmed, leading to errors during the ensuing DNA replication. The most frequent sperm DNA alteration in natural as well as in assisted reproduction involves an oxidative attack, leading to the formation of oxidized base adducts such as 8-hydroxy-2'-deoxyguanosine. We show here that not all the mouse chromosomes are equally susceptible to post-testicular sperm DNA oxidation. Mouse chromosome 19, the Y chromosome and the mitochondrial DNA were found most sensitive to oxidative attack most likely because of their position in the compacted sperm nucleus and because of the unprotected nature of the small mitochondrial genome. Bioinformatics analyses of sperm chromosomal regions and sequences susceptible to oxidation have indicated sequence features linked with embryonic development. Oxidative alterations of the paternal genome that are not efficiently repaired by the oocyte or not compensated by the maternal genome, may partly explain the low efficacy of assisted reproductive technologies. It also emphasizes the risk of transgenerational effects that may be increased when fertilization involves such spermatozoa showing high oxidative DNA damage.