Resistance to gastrointestinal nematodes has previously been shown to be a moderately heritable trait in some breeds of sheep, but the mechanisms of resistance are not well understood. Selection for resistance currently relies upon faecal egg counts (FEC), blood packed cell volumes, and FAMACHA scores, a visual indicator or anaemia. Identifying genomic markers associated with disease resistance would potentially improve the selection process and provide a more reliable means of classifying and understanding the biology behind resistant and susceptible sheep. A genome-wide association study (GWAS) was conducted to identify possible genetic loci associated with resistance to Haemonchus contortus in Katahdin sheep. Forty animals were selected from the top and bottom ten percent of estimated breeding values for FEC from a total pool of 641 sires and ram lambs. Samples were genotyped using the Applied BiosystemsTM AxiomTM Ovine Genotyping Array (50K) consisting 51,572 single nucleotide polymorphisms (SNPs). Following quality control, 46,268 SNPs were included in subsequent analyses. Analyses were conducted using a linear regression model in PLINK v1.90 and a single locus mixed-model in SNP and Variation Suite. Using linear regression, loci on chromosomes 2, 3, 16, and 23 were significantly associated at the genome level with FEC estimated breeding values, and we identified a single region on chromosome 2 that was significant using both statistical analyses. We suggest a potential role for the gene DIS3 like 3'-5' exoribonuclease 2 for gastrointestinal nematode resistance in Katahdin sheep, although further research is needed to validate these findings and elucidate the mechanisms involved.