Background: Congenital anomalies are conditions of prenatal origin that are present at birth, potentially impacting an infant's health, development and survival. The birth of a newborn with congenital anomalies imposes financial and emotional burdens on families. The aim of this study was to investigate the epidemiology of congenital anomalies in 2014 in Zabol, Iran.   Methods: This cross-sectional study was carried out in the Amir Al-Momenin Hospital between May of 2013 and April 2014. All the live born were included, and we have examined all newborns for the presence of congenital anomalies.   Results: During the twelve months, 9,309 newborns were included to the study. Of them, 72 (0.8%) newborns were affected with a congenital malformation. The congenital anomalies affected significantly higher proportion of male newborns (66.7%) than female newborns (33.3%). Among of them, musculoskeletal system abnormalities account for 45.9% of the total abnormalities allocating the highest frequency to itself. Subsequently, central nervous system abnormality (19.4%), gastrointestinal anomaly (15.3%), urinary tract abnormality (9.7%), chromosomal abnormality (2.8%), and multiple anomalies (1.4%) were frequent, respectively.   Conclusion: This study showed that prevalence of congenital anomalies is restively high in Zabol city. The results of this study identify the necessity of genetic counseling and early diagnosis to prevention, care and surveillance.