The hypovitaminosis D epidemic is a global health problem. Our aim was to assess the prevalence and potential risk factors of hypovitaminosis D among pregnant women on the eastern Mediterranean coast. Cross-sectional analysis involved 793 healthy pregnant women (35.3 ± 5.0 years) participating in ECLIPSES, a multicenter randomized trial. Socio-demographic, obstetric, anthropometric, lifestyle, dietary variables and blood draw was collected in the first trimester. Vitamin D deficiency was identified in 50.2% and insufficiency in 30.3% of pregnant women. The mean vitamin D level in the overall sample was 33.9 nmol/L (SD, 17.0). Multivariable logistic regression analysis applying AIC-based backward selection identified excess weight during the 1st trimester (BMI ≥ 25 kg/m2) (OR = 1.950, 95% CI = 1.409, 2.699), Arab ethnic group/dark skin colour (OR = 4.005, 95% CI = 2.488, 6.447), winter/spring (OR = 4.319, 95% CI = 3.112, 5.994), and consumption of milk (OR = 0.754, 95% CI = 0.572, 0.993) and yogurt (OR = 0.635, 95% CI = 0.436, 0.922) as independent risk factors for vitamin D deficiency. All of these factors (except yogurt consumption) and physical activity were independently associated with vitamin D deficiency/insufficiency risk in the final multivariable model (all p < 0.05). All these factors and social class were the most important determinants of circulating 25(OH)D concentrations. Our results confirm a high prevalence of vitamin D deficiency and insufficiency among pregnant women from the eastern Mediterranean coast.