This study focused on haplotype effects and linkage disequilibrium (LD) for the K232A locus and the promoter VNTR in the DGAT1 gene. Analyses were carried out in three German Holstein Frisian populations (including 492, 305, and 518 animals) for milk yield, milk fat and protein yield, and milk fat and protein content. We found that effects of the promoter VNTR were not significant and explain only a small amount of the variation of the QTL on BTA14. Haplotype effects were less significant than the K232A locus by itself, but the haplotype containing the A allele of the K232A locus and allele 3 with five repeats of the promoter VNTR showed negative effects on protein content when paternally inherited, whereas the haplotype with the A allele and VNTR allele 2 (with six repeats) increased the protein content. Significant differences between these two haplotypes occurred for protein yield as well, pointing to a linked effect that is picked up by the haplotypes rather than a direct effect of the VNTR. The linkage disequilibrium, estimated by D', showed values between 0.29 and 0.59 which is unexpectedly low for a distance of ~10 kb. Only a very low correlation between the two loci was observed due to the almost similar frequencies of haplotypes containing the A or K allele of the K232A locus.