Adequate vitamin D status during pregnancy is important for developing fetal bone strength and density and may play a role in preventing a range of skeletal and non-skeletal diseases in both mothers and children. We previously identified Mongolian women of reproductive age to have the lowest vitamin D levels yet observed in any population globally, which renders this population uniquely important in vitamin D research. In this study, we measured the seasonal distribution of 25-hydroxyvitamin D (25(OH)D) concentration in 390 healthy third trimester pregnant women living in urban and rural Mongolia using DiaSorin LIAISON and compared this distribution to that of 206 third trimester women living in Boston, USA. Also, we analyzed seasonally-independent associations between (25(OH)D) levels and selected predictors in both groups using quantile regression. Mean 25(OH)D levels were significantly higher and less seasonal in Boston (seasonal range: 27.1 ± 7.0–31.5 ± 7.7 ng/ml) than in Mongolia (seasonal range: 11.2 ± 3.9–19.2 ± 6.7 ng/ml). Adjusting for month of blood draw, higher 25(OH)D levels were significantly associated with older age, lower gravidity, lower BMI, and lack of a college or university degree among Boston participants, however, only gravidity was robust to multivariable adjustment. No assessed characteristics were independently predictive in Mongolia, likely due to universally low 25(OH)D levels and a resulting lack of between-person variation. In conclusion, vitamin D status among pregnant Mongolians is severely depressed throughout the year and should be addressed through fortification and supplementation, while in the U.S., deficiency is associated with specific characteristics targetable through supplementation.