The objective of this study was to identify QTL associated with the breeding value of somatic cell count (SCC) using a genome-wide association approach for Holstein breed in Portugal. Genotypes of 526 sires were obtained using the Illumina-BovineSNP50-BeadChip. Atotal of 37,031 SNPs spanning across 29 autosomes were validated for the quality control. The haplotype blocks and linkage disequilibrium (LD) were estimated between close significant SNPs (500 kb between significant SNPs). Thirty-four significant SNPs association were identified on 16 different chromosomes. Eighteen of these SNPs were significantly (P < 1 x10-4) associated with SCC at suggestive threshold level, and the remained 16 SNPs are significant (P < 5 x 10-5) associated with SCC at genome-wide threshold level. The results of our study are in line with previous studies with evidence supporting new QTLs for SCC. Numerous of the associated SNPs were found within or near regions containing candidate genes. Seven SNPs were found in the intronic region of candidate genes; NCOA2 on BTA 14, ANKFN1 on BTA 19, PARP8 on BTA 20, SEMA5A on BTA 20, LOXHD1 on BTA 24, LCMT1 on BTA 25 and SH3PXD2A on BTA 26. One SNP was found in the downstream of GJC3 gene on BTA 25, and the remaining of SNPs were found in the intergenic region of different genes.