There are few recent data on the prevalence of substance abuse among Danish pregnant women. During 2013, in the Region of Southern Denmark, a cross-sectional, anonymous, screening-based study was conducted among pregnant women attending for routine ultrasound scan at 12 weeks gestation. The women submitted a urine sample and completed a short questionnaire. Urine samples were tested for opiates, cannabis, benzodiazepines, cocaine, methadone, amphetamine and methamphetamine. Positive samples underwent repeat analysis for confirmation. Of 690 pregnant women, 88.1% participated. Overall, 3.6% of women had a positive urine sample confirmed by repeated analysis. The age distribution in women with positive samples did not differ from the entire cohort. Our findings indicate a larger prevalence than anticipated, and that a substantial number of pregnant women with substance abuse are not appropriately referred to the focused specialist center for such women at risk.