This study aimed to identify putative quantitative trait loci (QTL) that significantly affect internal parasite resistance in a backcross sheep population. A Romney x Merino backcross (to Merino) flock was challenged in 3 separate infections with Trichostrongylus colubriformis (primary and secondary) and Haemonchus contortus (tertiary). Haematological parameters were measured and faecal worm egg counts (FWEC) were established to estimate parasite burden. QTL mapping was conducted for FWEC and for the changes in haematocrit following H. contortus challenge and in eosinophil numbers following T. colubriformis challenge. Animals were genotyped for 55 microsatellite markers on selected chromosomes 2, 3, 6, 11, 13, 15, 21, and 22. Four putative quantitative trait loci were found; these being for eosinophil change in the primary infection (OAR 21), for FWEC in the first infection and eosinophil change in the secondary infection (OAR 3) and for FWEC in the secondary infection (OAR 22). No significant quantitative trait loci were detected for FWEC or haematocrit change during the Haemonchus contortus infection. The position of the putative quantitative trait loci for eosinophil change on OAR 3 is consistent with other reports of parasite resistance quantitative trait loci, implying some commonality between studies.