Susceptibility to developing CD is widely accepted to be primarily associated with a particular HLA-DQ alpha beta heterodimer encoded by the DQA1*0501 and DQB1*0201 alleles in cis position on the DR3,DQ2 haplotype or in trans position by DR5,DQ7/DR7,DQ2 heterozygotes. We performed genomic HLA-DR and -DQ typing of 100 unrelated Spanish celiac children and 180 ethnically matched controls. As expected, most (92 out of 100) celiac patients carried the HLA-DQ alpha beta heterodimer, and we selected these individuals for further studies. The results corroborate that although the DQA1*0501 and DQB1*0201 genes in single dosage appear sufficient for conferring disease susceptibility, individuals homozygotes for DQB1*0201 show an increased risk. Furthermore, our data also show that those carrying the genotype DR5,DQ7/DR7,DQ2 have a significantly increased risk of developing CD as compared to those that are non-DR7 positive, also carrying the CD-associated HLA-DQ alpha beta heterodimer. This strongly suggests that there is an MHC linked non-HLA-DQ gene primarily associated with CD present on DR7,DQ2 haplotype, which should either be DR7 or in strong linkage disequilibrium with it. Our data also indicate that, as has already been suggested, another HLA-associated CD susceptibility gene may be present on some DR4-carrying haplotypes.