Background and Objectives: Congenital anomalies can increase the neonatal mortality rate. Infants with anomalies suffer from long-term disabilities that impose heavy burdens on their families and healthcare systems. Understanding the prevalence of congenital anomalies helps health policy-makers develop better health-related policies. This study aimed to evaluate the prevalence of major congenital anomalies among live births in Birjand city, Iran. Methods: This cross-sectional descriptive-analytical study was conducted on 6,000 infants who were born from September 23, 2015, to March 6, 2016, in the maternity departments in Birjand. Stillbirths and infants who died immediately after birth, i.e. before the assessment for anomalies, were excluded. On the first day of birth, a neonatologist or a pediatrician performed a careful physical examination for each infant to diagnose probable congenital anomalies. Appropriate diagnostic procedures were also used to confirm the diagnosis when needed. Then, data on the characteristics of infants were collected using a researcher-made checklist. The data were reported using descriptive statistics such as absolute frequency, relative frequency, mean, and standard deviation. Moreover, the Chi-square and Fisher's exact tests were conducted using the SPSS computer program (v. 16.0) for hypothesis testing at a significance level of less than 0.05. Results: The prevalence of major congenital anomalies was 1.83 cases per 1000 live births. The prevalence rates of low birth weight and prematurity were significantly greater among infants with congenital anomalies than in their non-afflicted counterparts (45.5% vs. 15.9% and 36.4% vs. 11.1%, respectively; P < 0.05). Around 63.6% of the anomalies were among male infants and 54.5% of parents had kinship relationships. Conclusions: This study showed that the prevalence of major congenital anomalies among live births in Birjand was 1.83 cases per 1000 live births, which is less than the rates reported in other areas of Iran.