Background: Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies (GWAS). Nevertheless, currently few underlying molecular mechanisms of complex disease are known. Our approach has been to investigate whether variation in binding of a transcription factor, the vitamin D receptor (VDR) whose activating ligand vitamin D has often been proposed as a modifiable factor in multiple disorders, could explain any of these associations. VDR modifies gene expression by binding DNA as a heterodimer with the Retinoid X receptor (RXR). Results: We identified 43,332 genetic variants significantly associated with altered VDR binding affinity (VDR-BVs) using a high-resolution (ChIP-exo) genome-wide analysis of 27 HapMap lymphoblastoid cell lines (LCLs). The VDR-BVs are over-represented in well conserved consensus RXR::VDR binding motifs. However, most fell outside of recognisable RXR::VDR motifs, implying that genetic variation often affects RXR::VDR binding affinity only indirectly. Finally, we compared 341 VDR-BVs replicating by position in multiple individuals against background sets of variants lying within VDR-binding regions that had been matched in allele frequency and were independent with respect to linkage disequilibrium. In this stringent test, these replicated VDR-BVs were significantly (q < 0.1) and substantially (> 2-fold) enriched in GWAS intervals associated with autoimmune and other diseases, including inflammatory bowel disease, Crohn's disease and rheumatoid arthritis. Conclusions: Our findings are consistent with altered RXR::VDR binding contributing to immunity-related diseases. Replicated VDR-BVs associated with these disorders could represent causal disease risk alleles whose effect may be modifiable by vitamin D levels.