Background: Congenital malformations are among the most pressing health concerns globally. In Morocco, minimizing the morbidity and mortality associated with congenital malformations is a key health policy objective. In the Marrakech-Safi region, the prevalence and etiology of congenital malformations remain unclear. Objectives: This study seeks to ascertain the prevalence of clinically evident congenital malformations and identify the factors contributing to their incidence in the Marrakech-Safi region. Methods: A retrospective study was conducted in the maternity ward of the Mohamed VI University Hospital Center in Marrakech in 2022. An obstetric chart was utilized to gather sociodemographic, obstetrical, maternal, and neonatal data from the target population, including risk factors. The data were analyzed using SPSS 21 software. Results: Out of 17 250 files reviewed, 159 births with malformations were identified, resulting in a prevalence of 0.92% of births. Newborns with multiple malformations constituted 22.64% of all cases, with a prevalence of 2.08/1000 births. Neural tube defects were the most common, with a prevalence of 3.65/1000 births, followed by musculoskeletal defects and digestive tract defects. Chromosomal malformations, specifically trisomy 21, were the fifth most common, with a prevalence of 1.4/1000 births. Facial and urogenital malformations were the least frequent in this study. The occurrence of congenital malformations in this region is influenced by various risk factors, including maternal age, male sex, parity, medical history, and newborn weight at birth. Conclusions: In the Marrakech-Safi region, congenital malformations are influenced by a wide range of risk factors. Identifying these factors is crucial for healthcare providers to enhance surveillance among at-risk populations and develop effective preventive, diagnostic, and therapeutic strategies.