In 2007, a human Q fever epidemic started, mainly in the south eastern part of The Netherlands with a suspected indirect relation to dairy goats, and, to a lesser degree, to dairy sheep. This article describes the Q fever prevalences in Dutch dairy goat and dairy sheep bulk tank milk (BTM) samples, using a real-time (RT) PCR and ELISA. Results of BTM PCR and ELISA were compared with the serological status of individual animals, and correlations with a history of Q fever abortion were determined. When compared with ELISA results, the optimal cut-off value for the RT-PCR was 100 bacteria/ml. In 2008, there were 392 farms with more than 200 dairy goats, of which 292 submitted a BTM sample. Of these samples, 96 (32.9 per cent) were PCR positive and 87 (29.8 per cent) were ELISA positive. All farms with a history of Q fever abortion (n=17) were ELISA positive, 16 out of 17 were also PCR positive. BTM PCR or ELISA positive farms had significantly higher within-herd seroprevalences than BTM negative farms. In the south eastern provinces, the area where the human Q fever outbreak started in 2007, a significantly larger proportion of the BTM samples was PCR and ELISA positive compared to the rest of The Netherlands. None of the BTM samples from dairy sheep farms (n=16) were PCR positive but three of these farms were ELISA positive. The higher percentage of BTM positive farms in the area where the human Q fever outbreak started, supports the suspected relation between human cases and infected dairy goat farms.