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A major human Q fever epidemic occurred in The Netherlands during 2007–2009. In response, all pregnant goats from infected herds were culled before the 2010 kidding season without individual testing. The aim of this study was to assess whether high risk animals from recently infected naive herds can be identified by diagnostic testing. Samples of uterine fluid, milk and vaginal mucus from 203 euthanized pregnant goats were tested by PCR or ELISA. The results suggest that testing followed by culling of only the high risk animals is not a feasible method for protecting public health, mainly due to the low specificity of the tests and variability between herds. The risk of massive bacterial shedding during abortion or parturition can only be prevented by removal of all pregnant animals from naive recently infected herds.