A PCR approach (transposon PCR) with primers based on repetitive transposon-like sequences, which — depending on the isolate — were found at a minimum frequency of 19 on the C. burnetii genome, was established for the highly sensitive and specific detection of C. burnetii. This study describes the analytical detection of C. burnetii in milk, which requires a special preparation method prior to PCR. Because of the low level of C. burnetii particles in milk samples, template DNA was concentrated by a factor of 200, using cetyltrimethylammonium bromide as the precipitation reagent. Using this particular preparation method, even a single C. burnetii particle could be detected in 1 ml milk.