Several studies have shown that polymorphisms of clock genes are associated with diurnal preferences. We investigated whether other polymorphisms also are related to diurnal preference. Our examination targeted the region around the phosphorylation site of hPer2, as a previous report has shown that one single nucleotide polymorphism (SNP) at this site causes familial advanced sleep phase syndrome. We found three other SNPs in this region, with one synonymous SNP significantly correlated to diurnal preference in a healthy population. Although no functional relevance was predicted, this result indicates that diurnal preference in a healthy population is associated with this synonymous SNP of the hPer2 gene.