The association between the VDR SNPs (ApaI, TaqI, FokI, BsmI, and Cdx2) and changes in response was assessed. Cdx2 genotypes AA and GA, compared to GG, showed higher plasma levels of MMP9; BsmI bb genotype showed a greater decrease in circulating TNF-α levels after vitamin D3 supplementation; VDR genetic polymorphisms were not associated with longitudinal changes in the remaining cancer biomarkers. In breast cancer survivors with low 25(OH)D plasma levels and vitamin D3 supplementation changes in certain inflammatory biomarkers may be affected by VDR SNPs and haplotypes. Here, MMP9 is linked to breast cancer.