BackgroundVitamin B12 deficiency is associated with many adverse health outcomes and is highly prevalent worldwide. The present study assesses the prevalence and socio-demographic factors associated with vitamin B12 deficiency in a representative sample of pregnant women in Colombia.MethodWe used data from the cross-sectional, nationally representative survey (ENSIN, 2010). A total of 1.781, (13–49 years old) pregnant women were enrolled. Serum Vitamin B12 a concentration was determined by chemiluminescence and sociodemographic date was assessed by computer-assisted personal interview technology. Multivariate analyses using unordered multinomial logistic regression models were conducted in the main analysis.ResultsVitamin B12 concentrations ranged from 45 to 1000 pg/mL (mean 299.2 pg/mL, 95 % CI 290.6 to 303.7 pg/mL). A total of 18.6 % of pregnant women had vitamin B12 concentrations below 200 pg/mL and 41.3 % had concentrations between 200 and 300 pg/mL. Being of indigenous ethnicity, living in the east and living in a rural area showed the lowest mean values (273.2 pg/mL, 270.8 pg/mL and 290.1 pg/mL, respectively). The multivariate logistic regression shows that pregnant women belonging to the indigenous ethnic group OR 2.2, (95 % CI 1.1 to 4.3), living in the pacific region (west) OR 4.4, (95 % CI 2.8 to 6.9), or national territories (south) OR 2.3, (95 % CI 1.4 to 3.7) were associated with a higher probability of serum vitamin B12 deficiency.ConclusionThe prevalence of vitamin B12 deficiency in Colombian pregnant women is substantial. Factors associated with depletion among pregnant women should be considered for future interventions in countries experiencing nutritional transition.