The spectrum of congenital vertebral defects varies from benign lesions to severe, life-threatening conditions. The etiology and maternal risk factors remain mainly unclear in isolated cases. Hence, we aimed to assess and identify potential maternal risk factors for these anomalies. Based on previous studies, we hypothesized that maternal diabetes, smoking, advanced maternal age, obesity, chronic diseases, and medication used during the first trimester of pregnancy might increase the risk of congenital vertebral malformations. We performed a nationwide register-based case-control study. All cases with vertebral anomalies (including live births, stillbirths, and terminations for fetal anomaly) were identified in the Finnish Register of Congenital Malformations from 1997 to 2016. Five matched controls from the same geographic region were randomly selected for each case. Analyzed maternal risk factors included age, body mass index (BMI), parity, smoking, history of miscarriages, chronic diseases, and prescription drugs dispensed during the first trimester of pregnancy. In total, 256 cases with diagnosed congenital vertebral anomalies were identified. After excluding 66 malformations associated with known syndromes, 190 nonsyndromic malformation cases were included. These were compared with 950 matched controls. Maternal pregestational diabetes was a significant risk factor for congenital vertebral anomalies (adjusted odds ratio [OR], 7.30 [95% confidence interval (CI), 2.53 to 21.09). Also, rheumatoid arthritis (adjusted OR, 22.91 [95% CI, 2.67 to 196.40]), estrogens (adjusted OR, 5.30 [95% CI, 1.57 to 17.8]), and heparins (adjusted OR, 8.94 [95% CI, 1.38 to 57.9]) were associated with elevated risk. In a sensitivity analysis using imputation, maternal smoking was also significantly associated with an elevated risk (adjusted OR, 1.57 [95% CI, 1.05 to 2.34]). Maternal pregestational diabetes and rheumatoid arthritis increased the risk of congenital vertebral anomalies. Also, estrogens and heparins, both of which are frequently used in assisted reproductive technologies, were associated with an increased risk. Sensitivity analysis suggested an increased risk of vertebral anomalies with maternal smoking, warranting further studies. Prognostic Level III . See Instructions for Authors for a complete description of levels of evidence.