Balancing rapid genetic progress and maintenance of adequate genetic diversity has become one of the major challenges of the dairy industry worldwide. The loss of genetic diversity can be monitored using the inbreeding coefficient. Inbreeding increases the proportion of loci that are homozygous throughout the genome, some of which causes homozygosity of recessive alleles that negatively affect an animal’s performance. This phenomenon is known as inbreeding depression and tends to be most pronounced on fitness-related traits, such as male fertility. Traditionally, inbreeding has been monitored using pedigree information, or more recently, genomic data. Alternatively, the loss of genetic diversity can be quantified using runs of homozygosity (ROH), i.e., contiguous lengths of homozygous genotypes observed in individual chromosomes. The objective of this study was to evaluate the association between ROH and sire conception rate (SCR). The ROH were evaluated using about 300k genetic markers in 11,790 US Holstein bulls. Interestingly, the sum, mean, and maximum length of ROH were negatively associated with bull fertility. The association analysis between ROH and sire fertility was performed comparing 300 high-fertility vs. 300 low-fertility bulls. Both the average and sum of ROH length were significantly higher in the low-fertility group. The enrichment of overlapping ROH regions in low-fertility bulls was assessed using a Fisher’s exact test. Eight different ROH regions were significantly enriched in low-fertility bulls. Notably, these regions harbor many genes that are only expressed in testis or are reported in the literature to be responsible for male infertility. The results of this study can help not only to manage inbreeding in genomic selection programs by designing custom mating schemes, but also to better understand the mechanisms underlying male fertility.