Background <p>Consanguinity occurs widely in the Middle East and is associated with reproductive loss, congenital malformations, metabolic disorders, and autosomal recessive disorders. Qatar has a high consanguinity rate; however, large-scale population-based studies evaluating perinatal outcomes are lacking.</p> Methods <p>A retrospective cohort study of pregnancies ≥ 20 weeks of gestational age in Qatar from a maternity registry was conducted. Women were divided into consanguineous unions (CU) and non-consanguineous unions (NCU) based on their relationship with their spouses. The CUs were further divided into first-degree and second-degree. The outcomes included congenital anomalies, chromosomal anomalies, preterm births, stillbirths, neonatal deaths and small for gestational age (SGA).</p> Results <p>The rate of consanguinity among the women in the cohort was 30.8% (46.4% among Qatari women), with higher rates of first-degree (74%). Younger maternal age, obesity, higher parity and lower maternal education were factors associated with CUs. The incidences of anomalies, stillbirth and neonatal deaths in CUs were 21, 4.3 and 2.4 per 1000 births, respectively. After adjusting for confounders, CUs had higher odds of major congenital anomalies (aOR = 1.37; <i>p</i> = 0.049), stillbirth (aOR = 3.10, <i>p</i> = 0.007) and neonatal deaths (aOR = 3.15, <i>p</i> = 0.042) in non-anomalous babies, the difference being larger in non-Qatari women. Cardiovascular anomalies were most common, higher in first-degree CU, with nervous system anomalies higher in expatriates.</p> Conclusions <p>This study concludes that consanguinity is associated with an array of major risks, including congenital anomalies, stillbirths, and neonatal deaths, even in morphologically normal babies. The results are intended to raise awareness about the consequences of CUs in the country, in order to improve the genetic constitution and long-term health of future generations.</p>