The etiology of selective immunoglobulin A deficiency (IgAD) is not yet unraveled, but genetics seem to play an important role. Defects in processes during B-cell differentiation into plasma cells could exist in these patients, turning the genes controlling these processes into interesting candidate genes for IgAD predisposition, as PRDM1 (encoding Blimp-1) and XBP1. We studied the involvement of several polymorphisms located in PRDM1 and XBP1 on IgAD susceptibility. We performed a case-control study with 331 Spanish IgAD patients and 717 healthy controls, by analyzing five single nucleotide polymorphisms (SNPs) in these genes. Genetic frequencies of the studied SNPs did not significantly differ between patients and controls, even after stratifying by the known human leukocyte antigen risk factors or clinical phenotypes. Interaction between PRDM1 and XBP1 to confer disease predisposition was not detected either. In conclusion, the polymorphisms studied in the PRDM1 and XBP1 genes do not seem to be involved in IgAD predisposition in the Spanish population.