Introduction: Coxiellosis, caused by the bacterium Coxiella burnetii, is a reportable disease in animals and humans in Switzerland. The number of cases in farm animals and humans has risen continuously in recent years. The aim of this work was to investigate abortions and stillbirths in goats with a focus on C. burnetii, to identify excretory routes which pose a zoonotic risk and the excretion time after an acute infection. Besides the submitted fetuses, does were screened with a serological antibody test. In addition, excretion via milk, faeces and vaginal mucus were investigated in dams with fetuses tested positive for C. burnetii at 14-day intervals.C. burnetii were isolated in 8 cases (3× in the placenta, 2× in the abomasum, 3× in the placenta and abomasum) of 13 examined stillbirths/abortions. Ten abomasums of goat kids and 8 placentas were examined using modified Ziehl-Neelsen staining (ZN) according to Stamp simultaneously with a real-time PCR. Four of 18 samples were false negative using modified ZN staining according to Stamp in contrast to real-time PCR. Seven does had serum antibodies against Coxiella. The excretion of C. burnetii persisted for 63 days in the milk, for 96 days in the vaginal mucus and for 96 respectively 114 days in two does monitored extensively. Intermittent excretion could also be observed in the milk during these 63 days. The present study showed that confirmation of disease, respectively transmission cannot be based on a single test. Only combined serological antibody test and real-time PCR examinations of birth material, milk, feces and vaginal mucus can result in a conclusive diagnosis. In addition, the examination using modified ZN staining according to Stamp is less sensitive and specific than the real-time PCR examination.