The consequences of the selection for genetic resistance to Scrapie, on the portion of the genome that is in gametic disequilibrium with the PRNP gene, are estimated by means of simulation procedures, with separated evaluations of the expected average changes in the chromosome 13 and in the rest. It is observed that the indirect effects induced by the selection favourable to ARR allele can be important along the whole genome, especially around the PRNP locus, and larger the quicker and more radical the selection is and the lower the initial frequency of ARR is as well. These results allow to advise selections with low intensity for favouring a presumptive therapeutic effect of ARR with the minimum genomic reorganization. Otherwise, important changes should be expected in the genetic structure of the populations in all type of traits with unpredicted direction and magnitude.