Six genomic regions affecting clinical mastitis were identified through a GWAS study with imputed BovineHD chip genotype data in the Nordic Holstein cattle population. The association analyses were carried out using a SNP-by-SNP analysis by fitting the regression of allele dosage and a polygenic component in a linear mixed model. A total of 90 bulls’ whole genomes were sequenced with a coverage > 10X. Sequence reads were aligned to the cattle reference genome and polymorphisms in candidate regions were identified when one or more samples differed from the reference sequence. The polymorphisms in the six QTL regions were imputed in 5,193 genotyped bulls using Beagle v3.3. After imputation and quality control there were on average 4,600 markers/Mbp. Association analyses with imputed sequence data were repeated for the targeted regions. Functional annotations of the variants were done using Variant Effect Predictor (VEP) vers. 2.6 using ENSEMBL vers. 67 databases. Candidate polymorphisms affecting clinical mastitis were selected based on their association with the traits and functional annotations. A strong positional candidate gene for mastitis resistance on chromosome-6 is the NPFFR2 which encodes neuropeptide FF receptor 2. Many neuropeptides participate in immune responses by acting as stimulators or inhibitors of macrophage activity. NPFFR2 also binds the prolactin-releasing-hormone, suggesting that NPFFR2 may play a role in prolactin secretion. On chromosome-20, Leukemia Inhibitory Factor Receptor Alpha (LIFR) emerged as a strong candidate gene for mastitis resistance. The LIFR gene is involved in acute phase response and is expressed in saliva and mammary gland.