Introduction The incidence rate of vitamin D deficiency is increasing throughout the world. We measured the incidence rate of vitamin D deficiency and fibroblast growth factor 23 (FGF23) levels in 12- to 13-year-old adolescents in Japan. Materials and methods A total of 492 adolescents (247 boys and 245 girls) from Japanese community enrolled in this study. 25 hydroxyvitamin D (25(OH)D) was measured with radioimmunoassay. In the subjects with low 25(OH)D levels (<= 20 ng/ml), intact parathyroid hormone (iPTH), calcium (Ca), phosphorus (P), albumin (Alb), alkaline phosphatase (ALP) and FGF23 were measured. Results 25(OH)D levels were significantly lower in girls (20.9 +/- 3.1 ng/ml) than in boys (22.2 +/- 3.3 ng/ml) (p < 0.0001). Fifty-five boys (22.3%) and 83 (33.9%) girls showed vitamin D deficiency (< 20 ng/ml). One-hundred eighty-six (75.3%) boys and 162 (66.1%) girls showed vitamin D insufficiency (>= 20 ng/ml, < 30 ng/ml). In the subjects whose 25(OH)D levels were <= 20 ng/ml, the levels of iPTH, Ca, P, Alb, ALP and FGF23 were 22.3 +/- 9.0 pg/ml, 9.5 +/- 0.4 mg/dl, 4.7 +/- 0.6 mg/dl, 4.6 +/- 0.3 g/dl, 920.8 +/- 339.3 U/l and 42.6 +/- 26.0 pg/ml, respectively. There was a significant negative association between serum 25(OH)D levels and iPTH [r = - 0.290 (p < 0.0001)]. There was no significant association between serum 25(OH)D levels and FGF23. Conclusion We show that 28% of Japanese 12- to 13-year-old early adolescents suffer from vitamin D deficiency. Findings from this study indicate that vitamin D deficiency requires close oversight in public health during adolescence to ensure proper bone health.