The effect of vitamin D supplementation on growth of fetal bones during pregnancy is unclear. The aim of this study was to assess the effect of low dose vitamin D supplementation during pregnancy on bony anthropometric aspects of the fetus. In this prospective randomized trial, 140 patients were divided into two equally matched groups according to age, 25(OH)D level, exercise, and dietary intake. Then 1000 IU per day vitamin D supplement was given to the intervention group while the control group received placebo. Then crown-rump length (CRL) and femur length (FL) during the first trimester and humerus and femur lengths as well as their proximal metaphyseal diameter (PMD), midshaft diameter (MSD) and distal metaphyseal diameter (DMD) in the second and third trimester were measured using ultrasonography technique. Finally, no significant difference was observed for CRL (p = 0.93). Although FL was not statistically significant in the first trimester (p = 0.54), its measurement in the intervention group and the control group in the second (28.87 ± 2.14 vs. 26.89 ± 2.08; p ≤0.001) and the third (65.31 ± 2.17 vs. 62.85 ± 1.94; p ≤0.001) trimesters was significantly different. Femoral PMD, MSD, and DMD measurement increased more in the intervention group in comparison with the control group with P values <0.05. HL measurement in the intervention group and the control group in the second (28.62 ± 1.94 vs. 27.23 ± 2.08; p ≤0.001) and the third (61.29 ± 2.84 vs. 59.85 ± 1.79; p ≤0.001) trimesters revealed significant differences. Humeral PMD, MSD, and DMD measurement increased in the intervention group in comparison with the control group with P values <0.001 for all. It is suggested to prescribe low dose vitamin D (1000 IU per day) from early pregnancy with possible increment in length and diameter of femur and humerus bones of the fetus.