In this study we explored the spatial variation of Bovine tuberculosis (BTB) risk of being positive, new positive or persistently positive, as well as the risk of eliminating BTB in positive herds throughout Spain from 2006 to 2009 by means of hierarchical Bayesian models. The results of the models showed that the risk of infection (positive or new positive herds), persistence and elimination was lower in counties located in north and north-eastern of Spain, and in the Balearic and Canary islands than in the rest of the country. In some counties the risk of positivity was high during the four years of study, whereas there were others where the risk of positivity was high only in some of the years. With regard to the risk of persistence of BTB positive herds, counties located in the central, western and south-western part of the country had a higher risk in the three studied periods. This study has identified some specific areas of increased BTB risk in Spain, information that is useful for disease management.