Holoprosencephaly (HPE) is one of the most common developmental field defects, occurring in 1 in 250 conceptuses and in 1 in 10,000–20,000 live births. Nearly half of patients with HPE have a recognized syndrome or a single gene defect. However, little is known about the risk factors for the remainder with “nonsyndromic” HPE. In our case–control study, we examine factors associated with nonsyndromic HPE. We identified 47 patients with HPE from the genetics clinic database with an equal number of controls matched for gender and birthdate. Of the 47 patients, 23 were identified as nonsyndromic. No statistically significant differences were noted between the mean maternal and paternal ages of patients and controls. Factors associated with nonsyndromic HPE were: having an Aboriginal mother (unadjusted odds ratio [OR] 3.5, 95% confidence interval [CI] 1.1–11.1), an Aboriginal father (OR 12.8, 95% CI 3.0–55.1), at least one Aboriginal parent (OR 5.0, 95% CI 1.6–16.0), or two Aboriginal parents (OR 8.8, 95% CI 2.0–37.8), the presence of a family history of a midline facial defect (OR 8.2, 95% CI 1.5–45.2), and being of low socioeconomic status (OR 3.0, 95% CI 1.0–9.1). Having an Aboriginal background remained statistically significant after adjusting for low socioeconomic status. Other associations evaluated—history of prior spontaneous abortion, stillbirth, neonatal death, prepregnancy diabetes, infections during pregnancy, alcohol exposure, smoking, and substance abuse—were not significantly associated with nonsyndromic HPE. The use of periconceptional folic acid or vitamins was not associated with a lower risk of nonsyndromic HPE. © 2012 Wiley Periodicals, Inc.