Coxiella burnetii seroprevalence was assessed on Dutch dairy and non-dairy sheep farms using ELISA. Risk factors for seropositivity on non-dairy sheep farms were identified at farm and sheep level by univariate and multivariate multilevel analyses. Based on 953 dairy and 5671 non-dairy serum samples, sheep seroprevalences were 18.7 per cent and 2.0 per cent, respectively, and 78.6 per cent and 30.5 per cent at farm level. Significant risk factors for non-dairy sheep farms were farm location in the south of the country, sheep kept on marginal grounds, one or several supply addresses for ewes during 2007–2009 and wearing farm boots and/or outfit by professional visitors. On sheep level, risk factors included among others farm location in the south of the country, lamb breeding as main farm purpose, goat density within 10 km farm radius, use of windbreak curtain or windshields, and presence of ≥6 stillborn lambs in 2009. Farm location in the south of the country and goat density suggests that infected goats have played a role in the transmission to non-dairy sheep. Other risk factors suggest introduction of the bacterium through sheep supply and professional visitors. Biosecurity measures should be strengthened, including avoiding infection during handling of stillborn lambs and birth products in the lambing period.