An attempt to balance selection intensity and conservation of genetic diversity was made in the national program for breeding for scrapie resistance in the Netherlands. The ARR allele is associated with resistance to scrapie. In the Netherlands a breeding program was started on a voluntary basis in 2001 and starting 2004 the use of ARR/ARR rams was obligatory. In some rare breeds there were so few ARR/ARR rams that the risk of high inbreeding and associated loss of genetic diversity would be unacceptably high. Based on computer simulations predicting the inbreeding rates for several breeds exemptions on the obligatory breeding program were allowed. In this paper the ARR frequencies and associated inbreeding rates are analyzed as an indication of loss in genetic diversity during the years of scrapie selection in two breeds: the “Zwartbles schaap” (Black-blazed sheep) and the “Melkschaap” (Friesian-Zealand Milksheep).