Since 2003 eleven Swiss sheep flocks were affected by abortion storms due to Salmonella abortusovis, an infection which had not been reported in this country for decades although cases of salmonellosis are notifiable in Switzerland. This raised doubts about the adequacy of the currently used diagnostic tools and the origin of this infection. Therefore, PCR was tested for its potential as a more rapid and more reliable method for diagnosing S. abortusovis infections under field conditions. Fecal and vaginal samples were collected at different times after abortion and PCR was used to detect bacterial DNA. Bacteria were isolated by conventional culture techniques. For determining their origin they were analyzed by pulsed field gel electrophoresis (PFGE) and compared to isolates from Germany and France. Sequencing of randomly selected amplicons allowed confirming the specificity of the result. PCR was more sensitive because it allowed detecting S. abortusovis DNA up to three months after infection even in samples that were negative by culture. Escherichia coli from the digestive tract of sheep could inhibit the growth of S. abortusovis in vitro suggesting that the lower sensitivity of diagnosis by bacterial culture may in part be due to growth inhibition of S. abortusovis by resident bacteria. Results of PFGE indicated that the Swiss strains were closely related among themselves but distinct from German and French strains suggesting the presence of an autochthonous infection.