Xanthinuria Type I is caused by mutations in the xanthine dehydrogenase gene (XDH). We report on a patient suffering from xanthinuria. Genomic DNA was screened for point mutations and imbalances in the XDH gene by sequencing and microarray typing. We could identify homozygosity of a multiexon deletion in the XDH gene; large genomic imbalances have not yet been reported in this disease. As our case and other studies on genetic alterations in kidney diseases show, large deletions (and duplications) significantly contribute to the etiology of these entities, specific assays to discover these imbalances should therefore be included in genetic testing approaches.