Lutein (L) and zeaxanthin (Z) are involved in visual function and could prevent age-related macular degeneration and chronic diseases and improve cognitive performances. Adipose tissue is the main storage site for these xanthophylls (Xanth). The factors affecting their concentrations in this tissue remain poorly understood but in animal models, genetic variations in apolipoprotein E and β-carotene oxygenase 2 have been associated with adipose tissue L concentration. Therefore, the aims of this study were to better characterize the interindividual variability of adipose tissue Xanth concentration and to identify single nucleotide polymorphisms (SNPs) associated with it. Periumbilical subcutaneous adipose tissue samples were collected on 6 occasions in 42 healthy adult males and L and Z concentrations were measured by HPLC. Participants had their whole genome genotyped and the associations of 3589 SNPs in 49 candidate genes with the concentrations of L and Z were measured. Mean L and Z concentrations were 281 ± 27 and 150 ± 14 nmol g -1 proteins, respectively. There was no significant correlation between plasma and adipose tissue Xanth concentrations, although the correlation for L approached significance (Pearson's r = 0.276, p = 0.077). Following univariate filtering, 109 and 97 SNPs were then entered into a partial least squares regression analysis to identify the combination of SNPs that explained best adipose tissue concentration of L and Z, respectively. A combination of 7 SNPs in ELOVL5, PPARG, ISX and ABCA1, explained 58% of the variability in adipose tissue L concentration while 11 SNPs located in or near PPARG, ABCA1, ELOVL5, CXCL8, IRS1, ISX, MC4R explained 53% of the variance in adipose tissue Z concentration. This suggests that some genetic variations influence the concentrations of these Xanth in adipose tissue and could therefore indirectly influence the health effects of these compounds. Clinical Trial Registry: https://ClinicalTrials.gov registration number NCT02100774.