Fertilisation with sperm harbouring damaged DNA can trigger de novo mutations in the embryo, deleteriously affecting embryo development and future offspring health. As such, it is vital that DNA integrity assessments are routinely conducted. Despite the range of DNA integrity assessments available, it remains unclear which assay holds greatest prognostic value. We therefore aimed to assess the ability of common DNA integrity assays to identify ill-fated pregnancies. To this end, dismount semen samples were collected weekly from 47 Thoroughbred stallions during the 2017 (n=486) and 2018 (n=318) breeding seasons. Samples were diluted (2:1,extender:semen), and purified to isolate the high-quality sperm fraction. Sperm concentration and motility were also recorded (iSperm™). Samples were subsequently fixed for 8-oxoguanine (8-oxoG) assessment via flow cytometry, or snap frozen for sperm chromatin structure assay (SCSA) and alkaline comet assessments. Pregnancy data were used to identify samples that were associated with successful pregnancies (healthy offspring produced), and those that were associated with ‘lost’ pregnancies (pregnancy confirmed at 14 days post-breeding, and subsequently lost). 8-oxoG fluorescence of sperm DNA was significantly higher in samples associated with a lost pregnancy, compared to successful pregnancies (P≤0.05). In support of this, comet tail fluorescence was also significantly higher in samples where the pregnancy was lost (61±2.3%), compared to those that produced a healthy offspring (50±5.1%;P≤0.01). However, no difference was detected via SCSA, with both groups recording a DNA Fragmentation Index of 1% (P≥0.05). These findings indicate the prognostic value of both the 8-oxoG and alkaline comet assays in identifying ejaculates that will likely result in lost pregnancies, alongside the vital importance of ensuring appropriate assessments of sperm DNA integrity are routinely conducted. Further research is required to assess the value of other DNA integrity assays and to understand the heritable genetic risks to offspring.