A common feature of male infertility is the production of spermatozoa that possess extensive oxidative DNA damage. Much of this damage appears to originate during the post-testicular maturation of spermatozoa, at a time when they are known to be particularly vulnerable to oxidative insult. In the case of human spermatozoa, the presence of oxidatively damaged DNA has been correlated with altered sperm motility and compromised fertilizing capacity. However, if these spermatozoa are able to successfully fertilise an oocyte then there is the potential for such damage to increase the risk of paternal genomic defects being inherited by the offspring. In this study, we have sought to determine whether the entire paternal genome is uniformly vulnerable to oxidative DNA damage or whether certain regions display differential sensitivity to this insult. For this purpose, spermatozoa from healthy normozoospermic donors were exposed to hydrogen peroxide for 1h. Following treatment, oxidatively damaged DNA fragments were isolated via a modified chromatin immunoprecipitation technique. The selectively immunoprecipitated DNA was then subjected to genome-wide sequencing and bioinformatic analyses to identify those regions that displayed the highest vulnerability. This approach revealed approximately 9,000 vulnerable regions, 150-1000bp in size, unevenly spread among all chromosomes, with specific chromosomes more susceptible to oxidative damage. Vulnerable sites correlated with regions of the genome lying outside the protamine and histone packaged domains. These sites were also strongly associated with SINE (short interspersed nuclear element) repeats, centromeres, telomeres and gene intronic regions close to transcription start sites. Gene ontology analysis of the genes residing inside and in close proximity to vulnerable regions, identified a number that were ubiquitously expressed and involved in ATP binding processes. The identification of genomic domains vulnerable to oxidative damage represents an important step in understanding the implications of this form of insult for both fertilisation and offspring development.