Coxiella burnetii is an obligate intracellular pathogen common in livestock on every continent. It is easily dispersed and highly infectious, but not extremely virulent. Infected animals shed the bacterial cells in bodily fluids such as urine and milk. Despite its ubiquity, C. burnetii is difficult to culture and thus difficult to genotype. As a result, little is known about its geographic distribution and population structure. While the pasteurization process kills this pathogen, DNA may still be present in quantities suitable for detection and genotyping. To test this hypothesis, 10 samples of bovine milk as well as 1 sample of goat milk, originating from 11 dairy plants across five states, were purchased from local grocery stores in Flagstaff, AZ. These samples underwent crude DNA extractions that were then tested using a C. burnetii detection assay: IS1111. All samples tested positive for C. burnetii DNA, suggesting that it is widely distributed in milk in the U.S. Genotyping was performed using TaqMan dual probe assays to target single-nucleotide polymorphisms. In most cases, genotyping data were obtained and demonstrated that all samples are phylogenetically similar, suggestive of a dominant genotype in U.S. dairies. We have demonstrated that detecting and genotyping C.burnetii from milk is possible, allowing for more broad and detailed epidemiological studies of this pathogen in the future.