This study aimed to identify quantitative trait loci associated with endoparasitic infection in Scottish Blackface sheep. Data were collected from 789 animals over a 3-year period. All of the animals were continually exposed to a mixed nematode infection by grazing. Faecal samples were collected in August, September and October each year at ca. 16, 20 and 24 weeks of age; Nematodirus spp. eggs were counted separately from the other species of nematodes. Blood samples were collected in October from which immunoglobulin A (IgA) activity was measured and DNA was extracted for genotyping. In total, 139 Microsatellite markers were genotyped across eight chromosomal regions (chromosomes 1, 2, 3, 5, 14, 18, 20 and 21) in the sires and progeny were genotyped for the markers that were polymorphic in their sire. Evidence was found for quantitative trait loci (QTL) on chromosomes 2, 3, 14 and 20. QTL associated with specific IgA activity were identified in chromosomes 3 and 20, in regions close to IFNG (chromosome 3) and the MHC (chromosome 20). QTL associated with Nematodirus FEC were identified on chromosomes 2, 3 and 14. Lastly, QTL associated with non-Nematodirus Strongyle FEC were identified on chromosomes 3 and 20. This study has shown that some aspects of host resistance to gastrointestinal parasites are under strong genetic control, therefore these QTL could be utilised in a marker-assisted selection scheme to increase host resistance to gastrointestinal parasites.