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The PER3 gene at 1p36.23 is likely to be component of the secondary human circadian rhythm clocks and codes for the 1201 amino acid period circadian protein homolog 3. It is mainly expressed in the cytoplasm.

The number of repeats of 18 amino acids in positions 966 to 1055 (i.e. a variable number tandem repeat) is polymorphic in man (not other mammals) and varies among at least 2 different alleles. Alleles corresponding in size to a 4 (PER3.4/PER34) and 5 (PER3.5/PER35) repeats are known. In most human populations around 10% of individuals are homozygous for the 5-repeat (PER35), whereas approximately 50% are homozygous for the 4-repeat (PER34). In some populations in Papua New Guinea the prevalence of the genotypes appears to be reversed. PER35 homozygotes have a morning preference, whereas homozygosity for the PER34 associates with evening preferences. PER35 homozygotes are vulnerable to sleep loss with a greater cognitive decline in response to total sleep deprivation[1]. Women with PER34 homozygousity are more at risk of anxiety with reduced sleep duration[2]. The G allele of rs228697 (P864A) in PER3 is more common in evening types than in morning types[3].