Methods and Results: We measured the concentrations of 25-OH vitamin D in the serum of Japanese patients with PFAPA. Serum levels of 25-OH vitamin D of the 14 subjects were 13.7 to 29.0 ng/mL, Five out of 14 subjects (35.7%) had levels less than 20 ng/ mL, which is assessed as vitamin D deficiency. There was a significant difference in serum vitamin D levels between the PFAPA syndrome group and the age-matched control group (P = 0.03). The levels of vitamin D of 16 PFAPA patients, 8 subjects with intractable otitis media and 11 healthy controls were measured. Serum levels of patients with PFAPA syndrome and intractable otitis media were significantly lower than those of controls. There was no statistically significant difference in the levels of 25- OH vitamin D with sex, fever, duration of the febrile period, serum level of amyloid A, and frequency of occurrence of aphthous stomatitis. However, the occurrence of aphthous stomatitis was more frequent in patients with low levels of 25-OH vitamin D compared with patients with higher levels. There was no specific polymorphism compared with controls and past genomic data in 6 candidates of SNPs of VDR.