Abstract Background The aim of this study was to estimate the seroprevalence of Coxiella burnetii in dairy goat farms in the Netherlands and to identify risk factors for farm and goat seropositivity before mandatory vaccination started. We approached 334 eligible farms with more than 100 goats for serum sampling and a farm questionnaire. Per farm, median 21 goats were sampled. A farm was considered positive when at least one goat tested ELISA positive. Results In total, 2,828 goat serum samples from 123 farms were available. Farm prevalence was 43.1% (95%CI: 34.3%-51.8%). Overall goat seroprevalence was 21.4% (95%CI: 19.9%-22.9%) and among the 53 positive farms 46.6% (95%CI: 43.8%-49.3%). Multivariable logistic regression analysis included 96 farms and showed that farm location within 8 kilometres proximity from a bulk milk PCR positive farm, location in a municipality with high cattle density (≥ 100 cattle per square kilometre), controlling nuisance animals through covering airspaces, presence of cats or dogs in the goat stable, straw imported from abroad or unknown origin and a herd size above 800 goats were independent risk factors associated with Q fever on farm level. At animal level almost identical risk factors were found, with use of windbreak curtain and artificial insemination as additional risk factors. Conclusion In 2009-2010, the seroprevalence in dairy goats in the Netherlands increased on animal and farm level compared to a previous study in 2008. Risk factors suggest spread from relatively closely located bulk milk-infected small ruminant farms, next to introduction and spread from companion animals, imported straw and use of artificial insemination. In-depth studies investigating the role of artificial insemination and bedding material are needed, while simultaneously general biosecurity measures should be updated, such as avoiding companion animals and vermin entering the stables, next to advice on farm stable constructions on how to prevent introduction and minimize airborne transmission from ...