Control and prevention of mastitis is a long standing goal of the dairy industry considering it affects 20 to 50% of any given herd and significantly decreases milk quality. Recent identification of genetic markers for mastitis have relied on somatic cell count (SCC) or clinical mastitis (CM) observation or averaged across a sire’s daughters. We propose utilizing novel phenotypes derived following an intramammary experimental challenge with S. uberis, which causes a high proportion of both clinical and subclinical mastitis cases. Aseptic milk samples were collected on each cow, n = 35 Holsteins, and used to determine both SCC and colony forming units (cfu) of S. uberis in milk. SCC was used to generate 3 novel phenotypes: area under the curve (AUC) of SCC for 0–7 d and 0–28 d post-challenge; and individual cows were placed in one of 3 categories (<21 d, 21–28 d, or > 28 d) based on when their SCC returned to below 200,000 cells/ml post-challenge. S. uberis cfu was used to create 4 additional phenotypes: S. uberis clearance S. uberis shedding cycles, and AUC of S. uberis cfu for 0–7 d and 0–28 d post-challenge. To identify loci of interest a 50K SNP chip analysis was performed using the BovineSNP50 v2 DNA Analysis BeadChip from Illumina and associations were tested using Plink. A total of 40 SNPs (P < 9.34 × 10⁻⁵) were identified across the 7 phenotypes. Of the SNPs identified, 12 are in regions with prior mastitis evidence lending validity to the use of our novel phenotypes to identify loci of interest. Furthermore, 14 of the SNPs identified are in genes with known functions linked to inflammation/immunity or regulation of gene expression, providing many potential candidate genes. These loci and candidate genes should be further investigated to identify potential roles in controlling S. uberis mastitis. Such investigations could lead to novel treatment or prevention compounds/protocols for S. uberis mastitis or genetic selection methods for cows with greater potential to resist S. uberis infection.