Tuberculosis caused by Mycobacterium bovis is a re- emerging disease of livestock which is of major economic importance world-wide, as well as being a zoonotic risk. There is significant heritability for host resistance to bovine tuberculosis (bTB) in dairy cattle. To identify resistance loci for bTB, we undertook a genome-wide association study in female Holstein-Friesian cattle with 592 cases and 559 age-matched controls from case herds. Cases and controls were categorised into distinct phenotypes: skin test and lesion positive versus skin test negative on multiple occasions, respectively. These animals were genotyped with the Illumina Bovine HD 700K bead chip. Genome-wide rapid association using linear and logistic mixed models and regression (GRAMMAR), regional heritability mapping (RHM) and haplotype-sharing analysis identified two novel resistance loci that attained chromosome-wise significance, in protein tyrosine phosphatase receptor T (PTPRT; P=4.8 x 10-7) and myosin IIIB (MYO3B; P=5.4. x 10-6). We estimated that 21% of the phenotypic variance in tuberculosis resistance could be explained by all of the informative SNPs, of which the region encompassing the PTPRT gene accounted for 6.2% of the variance and a further 3.6% was associated with a putative copy number variant (CNV) in MYO3B. The results from this study add to our understanding of variation in host control of infection and suggest that genetic marker-based selection for resistance to bTB has the potential to make a significant contribution to bTB control.