across all breeds within the on-farm study. However, this association did not persist within the Holstein-Frie- sian bull population. This discrepancy between the two studies may be a function of 1) differences in pheno- types and accuracy of phenotypes used (actual cow phe- notypic records adjusted for systematic environmental effects or predicted transmitting abilities), 2) differences in the parity of the progeny or period during which the phenotype was measured, 3) the mean performance of the animals or the environment they were exposed to (i.e. genotype by environment interaction) and 4) the different genetic background and breed of the animals in the study and how that may affect interactions between the polymorphism and background genes. It is worth noting that there was a lower frequency of TLR4- 2021 CT heterozygotes (0.26) in the Holstein-Friesian bull population than reported in the Holstein-Friesian cows (0.46). This discrepancy reflects the small sample size of the on-farm study. Flow cytometry analysis demonstrates that heterozy- gous AG animals of CD14-1908 have higher numbers of neutrophils expressing CD14 molecules [22]. This may confer the neutrophils with altered sensitivity to LPS [22] which may aid in their fight against pathogen attack. While no association with SCS was established within our study, to the authors’ knowledge this is the first report of the G allele of CD14-1908 associating with lower milk fat and protein yields and tending to associate with a decrease in milk production.