Different approaches were applied to investigate prion protein (PrP)-encoding gene effects on udder morphology and milk yield in Sardinian sheep. The PrP genotype of 23,077 animals (10,029 males) was determined. The direct effect of the PrP or a closely linked gene was analyzed at the population-wide level using 2 animal models, based on records from genotyped animals, including only the PrP genotype as a fixed effect. In the female model, the dependent variable was animal performance deviation, calculated as the sum of the individual random effects. The male model was based on daughter yield deviations. Both dependent variables were obtained from the national genetic evaluations of 2005. The significance of pairwise comparisons between genotypes was assessed by using the Tukey-Kramer multiple-comparison procedure. Within-family analyses were performed on sires heterozygous for the PrP gene to detect those genes that affect the traits of interest and are not in linkage disequilibrium with the PrP locus at the population-wide level. The overall results led us to exclude either a direct or a linkage gene effect of the PrP locus on udder morphology or milk yield in Sardinian sheep. A further analysis of males that neglected the relationship matrix was carried out to evaluate the effect on the loss of genetic gain of the different selection pressures applied on resistant and susceptible genotype classes. Significant differences between genotypes were detected for milk yield. These were due to the different selection pressures applied to the PrP genotype classes. Finally, no negative correlated genetic response on the selection traits is expected from the selection for scrapie resistance in the Sardinian breed. However, a loss of genetic gain for milk yield is likely to occur in the future due to the different selection pressures on resistant and susceptible males.