Introduction: It has been frequently suggested that overall genomic heterozygosity and, particularly, heterozygosity of loci on the so-called major histocompatibility complex (MHC), which is responsible for the recognition of foreign substances/ pathogens and the recognition of self and non-self, is associated with better health and better resistance to infections and parasites. It has further been speculated that such a potentially beneficial heterozygosity can be detected through body odor and facial attractiveness. Methods: On the basis of genome wide SNP data (713,014 SNPs) of participants from the Wisconsin Longitudinal Study, we therefore investigated whether homozygosity either on the MHC (measured as inbreeding coefficient) or genome-wide (measured as runs of homozygosity and inbreeding coefficient) is associated with rated facial attractiveness. Results: Although we found that the genome-wide average length of homozygous segments and the genome-wide inbreeding coefficient are significantly negatively associated with some measures of facial attractiveness, if corrected for multiple testing, any significant association was no longer formally significant after correction. In addition, the variance in facial attractiveness explained by the genome wide homozygosity is very low (<0.15%). We did not find any significant association between the inbreeding coefficient on the MHC and facial attractiveness. Discussion: We only find a weak association of genome- wide heterozygosity and facial attractiveness.