AbstractAlzheimer disease (AD) is heterogeneous and complex with a strong genetic diathesis. It is the most common cause of dementia affecting the elderly. Linkage studies [Kehoe et al., 1999; Hum Mol Genet 8: 237–245]; [Pericak‐Vance et al., 2000; Exp Gerontol 35: 1343–1352]; [Myers et al., 2002; Am J Med Genet 114: 235–244]; [Blacker et al., 2003; Hum Mol Genet 12: 23–32] identified chromosome 9q as a region containing a possible AD candidate gene. Functional protein studies [Mah et al., 2000; J Cell Biol 151: 847–862]; [Ko et al., 2002; J Biol Chem 277: 35386–35392] identified the UBQLN1 gene on chromosome 9q that encodes ubiquilin as a likely candidate for a role in late‐onset AD pathogenesis. A recent family‐based study by [Bertram et al., 2005; N Engl J 352: 884–894] reported genetic association and expression evidence for a putative AD risk allele of an intronic single nucleotide polymorphism (SNP) within the UBQLN1 gene. In this study, we comprehensively assessed whether any of seven polymorphisms located across the UBQLN1 gene are associated with AD in another large family‐based data set and an independent case‐control data set. We found no significant association of AD risk with any of the seven SNPs genotyped (including those SNPs previously reported by Bertram et al.) in either the family‐based or case‐control data set. Age‐specific analyses and analyses conditional on Apolipoprotein E (ApoE) genotype and sex also revealed no significant associations to AD risk in either data set. Using age at onset (AAO) as a quantitative trait revealed a modest age modifying association; however, the results were inconsistent between the data sets. Our results suggest that UBQLN1 variants do not increase risk for AD in these data. © 2006 Wiley‐Liss, Inc.