The importance of vitamin D for children's bone health has been well established, but the effects of less severe deficiency are not fully known. The main objective of this study was to assess the vitamin D status of Icelandic children at the age of 7, and again at 9 years of age, and the association of vitamin D status with bone mineral content and bone accrual over 2 years. We invited 321 children to participate in this study, and 267 (83 %) took part; 211 (79 %) underwent a DXA scan and 164 were again scanned 2 years later; 159 (60 %) vitamin D samples were measured and 119 (75 %) were measured again 2 years later. At age 7, 65 % of the children had vitamin D concentrations <50 nmol/l, and at age 9 this figure was 60 %. At age 7, 43 % of the children had insufficient amounts of vitamin D (37.5-50 nmol/l), and 22 % had a vitamin D deficiency (<37.5 nmol/l). In linear regression analysis, no association was found between vitamin D and bone mineral content. Furthermore, there was no significant difference in bone accrual over 2 years for the children with insufficient or deficient vitamin D at both ages, compared to those having more than 50 nmol/l at both time points. More than 60 % of Icelandic children have inadequate concentrations of vitamin D in serum repeatedly over a 2-year interval. However, vitamin D in the range did not have a significant effect on bone mineral content or accrual at ages 7 and 9.