Between October 2001 and December 2006 an estimated total of 6 million cattle in Japan were tested for BSE, with 31 returning a positive result. Exploratory mapping, the space-time scan statistic, and ordinal logistic regression have been used to describe the epidemiology of the 24 cases identified in the prefecture of Hokkaido, and to quantify the risk factors for the disease. Two birth cohort groups were affected: cattle born during a period of seven months in 1996, and cattle born between 1999 and 2001. The descriptive spatial analyses showed that eight of the 10 cases born in 1996 were born in areas with a relatively high density of dairy farms in the east of Hokkaido, but that the 14 later cases were more widely distributed throughout the prefecture, with equal numbers of cases in the east and the west. These findings provide indirect evidence of a single localised contamination of the cattle feed supply in 1996, and recycling of the infection after 1999.