In spite of suspected circadian differences between different ancestral groups, most human studies have used individuals of European descent. This also applies to three recent genome-wide association studies (GWAS), which pinpointed a number of chronotype loci. We investigated the distribution of these hits in different 1000 Genomes populations. We found 6 out of the 41 alleles previously identified by GWAS in European participants (in the genes RGS16, PER2 and AK5 and between the genes APH1A and CA14) to be absent from some non-European population groups. This highlights the need for ancestral diversity in circadian research and may reflect differences affecting the phenotype of individuals of East Asian ancestry.