The objective of this research was to explore the potential association between Coxiella burnetii shedding in milk and chronic subclinical mastitis in dairy cattle. In two separate studies, we identified an association between PCR-based detection of C. burnetii in milk and chronic subclinical mastitis in lactating dairy cows. These studies were conducted in a commercial dairy herd where there was ongoing intensive monitoring of subclinical mastitis by aerobic bacteriology, but no prior knowledge or management of C. burnetii infections. In a case-control study, quarter level C. burnetii status determined by real-time quantitative PCR (RT-qPCR) was strongly associated with chronic subclinical mastitis as measured by milk somatic cell counts. In a subsequent cross sectional study, 147 (45%) of 325 lactating cows were positive for C. burnetii by RT-qPCR of composite milk samples. In a generalized linear model, accounting for the effect of covariates including aerobic intramammary infection status, C. burnetii PCR status was a significant predictor of linear somatic cell count score. In agreement with a small number of previous reports, this research provides evidence that there may be mammary gland specific manifestations of C. burnetii infections in dairy cattle.