Bovine mastitis remains one of the costliest diseases affecting the dairy industry. Individual susceptibility to mastitis and severity of infection varies between animals and can only be partially explained by genetics. As such, understanding how genetic predisposition coordinately interacts with epigenetic modifications and environmental exposures is necessary to bridge the gap in missing heritability. The role of DNA methylation in regulating the response to bacterial lipopolysaccharide (LPS) was first determined by performing reduced representation bisulfite sequencing on fibroblasts isolated from heifers at 5- and 16-months of age that exhibit an age-dependent up-regulation in LPS-responsiveness. More than 14,000 differentially methylated sites were identified between the two sets of cultures with a trend towards decreased methylation with age. Young cultures were also hyper-methylated in gene promoters regulated by NF-κB and exhibited lower expression in genes that regulate the innate immune response, suggesting that methylation contributes to gene regulation in fibroblast innate response. Previously, TLR4 expression was shown to differ in the age-dependent fibroblast model, however, it was not known if variation in TLR4 expression would affect mastitis severity. Therefore, fibroblasts were isolated from sixty lactating, adult Holstein cows and their expression of TLR4, along with LPS-induced production of IL-8 and IL-6, was used to rank the animals from high to low. Six high responders and six low responders were then experimentally infected in one mammary gland with E. coli. Overall, severity of mastitis was quite variable, with a few notable differences between high and low responders. High responding animals had an earlier increase in somatic cell count and febrile response that coincided with more efficient bacterial clearance. However, tissue damage and milk production did not differ between the two groups, indicating that while rapid up-regulation of the innate response addresses bacterial clearance, subsequent down-regulation is required to alleviate damage within the mammary gland. Finally, one-week old bull calves were subjected to treatment with either saline or LPS to determine if neonatal exposure to endotoxin would make calves less responsive to a second LPS challenge at 32-days of age. The initial treatment showed a large effect of LPS as measured by higher plasma IL-6 and TNF-α concentrations in calves treated with LPS over saline. Subsequent treatment of all 10 calves with LPS showed a very similar response between the two treatment groups and significant inter-animal variability in clinical response. Fibroblasts and monocyte-derived-macrophages (MDMs) were also isolated following initial treatment to determine if any changes occurred at the cellular level as a result of LPS exposure. Fibroblasts isolated from calves at 20-days of age had a very low response to LPS that did not differ between the early life treatments. MDMs isolated from calves at 28-days of age were more responsive to LPS, but again no differences were detected between the early life treatments. In summary, our results suggest that DNA methylation likely plays a role in the cellular response to LPS and may partially contribute to differences between animals in severity of E. coli mastitis, however, the appropriate in vitro phenotype to detect susceptible animals still needs to be characterized before epigenetic biomarkers can be identified, and perhaps modified by environmental interventions.