Background: Birth defects are the leading cause of both neonatal and post-neonatal deaths, as an estimated 240,000 neonates die in their first month of life worldwide each year. In Iraq, local studies have shown varying frequencies and types of congenital anomalies. Objectives: To provide new insight into the incidence and types of congenital anomalies and to explore their possible risk factors in Baghdad City. Methods: In this cross-sectional observational study, a total of 2007 neonates were enrolled from six hospitals in Baghdad during the period extending between September and December 2020. Hospital records and personal interviews were used for data collection. These data included the neonates' demographic and clinical characteristics, maternal, pregnancy, and immediate postnatal conditions. Description of the defects in those with birth defects was recorded from hospital records and as described by the parents. Statistical analysis was performed as required. Results: There were 64 (3.2%) neonates with birth defects, i.e., an incidence of 32/1000 total births (28/1000 live births); of them, 38 (59.4%) were males, 8 (12.5%) were stillborn, 43 (66.2%) were born with a cesarean section, the majority (87.5%) had maternal age between 20 and 40 years, and 35 (54.6%) had a low birth weight and were statistically significant. In addition, reduced fetal movement, prematurity, and not receiving tonics during pregnancy were also statistically significant. Among the 64 births with congenital anomalies, multiple congenital anomalies were the most common defects [26 (40.6%)]. An isolated defect was detected in 38 (57.8%) of them. The predominant system involved was the gastrointestinal tract (GIT) [12 (18.8%)] cases, followed by the central nervous system (CNS) with 11 (17.2%) cases, and the musculoskeletal system (MS) with 6 (9.4%) cases. Conclusion: The incidence of birth defects in Baghdad is close to global figures at 28/1000 live births with multiple congenital anomalies, gastro-intestinal, central nervous, and musculoskeletal systems defects being the most frequent, while cardiovascular, genitourinary, and skin defects being the least frequent. Possible risk factors included maternal age, drug intake, and not receiving tonics during pregnancy.