Arylalkylamine N-acetyltransferase (AA-NAT) is a rate-limiting enzyme in melatonin hormone synthesis and participates in daily oscillations of the melatonin level. We studied the association between the AA-NAT gene and delayed sleep phase syndrome (DSPS). Results indicate that there is a significant difference in allele positivity at the single nucleotide polymorphism involved in an amino acid substitution from alanine to threonine at position 129 between patients with DSPS and healthy controls. The frequency of the 129 threonine allele is significantly higher in the patients than in the controls ( P=0.0029). The data suggest that AA-NAT could be a susceptibility gene for DSPS.