It has been suggested that the mites connected with the decay of stored hay may be involved in the transmission of scrapie, a neurological disorder in sheep. To find out whether there are any obvious differences in the mite fauna in hay that could be related to outbreaks of scrapie in sheep, we analysed the hay fauna from 23 farms in the Basque regions in France and Spain, areas with high and very low incidence of scrapie, respectively. We did find some differences in the composition of the fauna, and a species such as Pygmephorus spp. was more prevalent in scrapie-infected farms, and particularly in highly scrapie-infected farms. The former species is associated with late stages in the biological degradation of stored hay and could be linked to the disease. Besides being the first record of the composition of the hay mite fauna in Spain and France our finding of differences in mite communities in hay from scrapie versus non-scrapie farms is a further indication of the possible association of certain mite species with scrapie.