Background: In Morocco, there is no official data on the prevalence of congenital anomalies (CAs). Available data are mostly derived from hospital-based retrospective epidemiological analyses. Objectives: This study aims to describe the prevalence, distribution, and risk factors of CAs in the Beni Mellal-Khenifra region of central Morocco. Methods: Epidemiological data were obtained from delivery files of 163,842 births recorded by local medical services from January 2017 to December 2021. Additionally, a case-control study was conducted to analyze the risk factors. Results: The prevalence of CAs in this study area was 6.18 per thousand births. Musculoskeletal system anomalies were the most common (32.88%), followed by nervous system anomalies (22.20%). Genital organ abnormalities represented 7.37%, and cleft lip and palate accounted for 7.03%. Analysis by type of CA revealed that clubfeet were the most commonly reported anomalies in the study area, with a prevalence of 18%, followed by spina bifida (9%), anencephaly (7%), and cleft lips and palate (7.9%). The sex ratio (males/females) for all CAs was 1.24. Risk factors identified in this study included rural residency, maternal age over 35 years, parity, consanguinity, family history of CA, medication use before and during pregnancy, and infection episodes during pregnancy. Conclusions: The relatively high prevalence of congenital abnormalities in the Beni Mellal-Khenifra region highlights the need for prevention strategies through preconception care counseling and pregnancy monitoring, especially in rural areas. It is urgent to establish a teratovigilance registry in Morocco.