A quantitative trait locus (QTL) affecting milk fat and protein concentration was localized to a 4cM confidence interval on chromosome 6 centered on the microsatellite BM143. The genes and sequence variation in this region were characterized, and common haplotypes spanning five polymorphic sites in the genes IBSP, SPP1, PKD2, and ABCG2 for two sires heterozygous for this QTL were localized. Expression of SPP1 and ABCG2 in the bovine mammary gland increased from parturition through lactation. SPP1 was sequenced, and all the coding exons of ABCG2 and PKD2 were sequenced for these two sires. The single nucleotide change capable of encoding a substitution of tyrosine-581 to serine (Y581S) in the ABCG2 transporter was the only polymorphism corresponding to the segregation status of all three heterozygous and 15 homozygous sires for the QTL in the Israeli and US Holstein populations.