This study investigated associations of prion protein (PrP) genotype with body composition and weight traits of Scottish Blackface ewes. Body composition was predicted using computer tomography (CT) scans to estimate muscle, carcass fat, internal fat, and bone weights. The traits were measured at 4 key seasonal production points (pre-mating, pregnancy, midlactation, and weaning) over 4 production cycles (2 to 5 yr old). There were 2,413 records for each of the CT traits measured on 335 ewes, and 26,649 records for each of the body condition score and BW traits for 2,356 ewes. From 1999 to 2004, animals were genotyped to determine polymorphisms at codons 136, 154, and 171, which are associated with scrapie susceptibility. Four alleles were found in the population (ARR, AHQ, ARQ, and VRQ). The data were analyzed using a linear mixed random regression model assuming that the direct additive genetic effect was a 2nd order Legendre polynomial function of time. The PrP genotype was included in the model as a fixed effect along with other fixed factors with significant effects (P < 0.05). Five separate analyses were carried out for each trait, depending on the method of classifying the PrP genotype. In the first analysis, animals were categorized according to the genotype. Only the 5 most common genotypes (ARR/ARR, ARR/AHQ, ARR/ARQ, AHQ/ARQ, and ARQ/ARQ) were included. In the last 4 analyses, animals were categorized according to the number of each PrP allele carried. For CT traits and body condition score, results showed that the PrP genotype has no association with the overall mean of the traits (averaged over age). For BW, ewes without the ARQ allele were at least 0.5 kg heavier than ARQ homozygous and heterozygous ewes. On the other hand, there was a significant interaction between PrP genotype and age of the ewe (i.e., the effect of PrP genotype was not the same at different ages for 5 out of the 6 traits studied). In general, ARQ carrying ewes mobilized more fat reserves at times of nutrient deficiency, such as during lactation, and gained it back more quickly by the mating season (when nutrients became abundant) than non-ARQ carriers. Therefore, selecting against this allele would have consequences on BW and seasonal mobilization of body reserves. The number of VRQ alleles (the most scrapie susceptible allele) carried was not significantly associated with any of the traits.