Background and Aim: Along with extensive control of communicable diseases and decrease in their prevalence, congenital anomalies (CA) has grasped much attention in recent years. Almost 20% of babies’ mortality under one year of age is associated with CA. The present study was conducted to determine the percent of newborns with CA under Birjand city health centers. Materials and Methods: In this descriptive-analytical and retrospective study all newborns with CA under Birjand city health centers during 2007-2012 . were studied. Necessary data was collected by meansw of a researcher- designed questionnaire .whose content validity had already been confirmed. . The obtained data was analyzed using SPSS software ( version 16) and Kruskal Wallis descriptive analytical statistical test at the significant level α=0.05. Results: Out of 22076 newborn babies during 2007-2012, 118 cases had CA ( CA prevalence . was 5.34%). . It was found that CA was more prevalent in boys than in girls (55.9% vs. 44.1%).The babies’ parents were mainly (58.5%) relatives .. Congenital heart diseases (36.5%) and musculoskeletal disorders (16.1%) were accounted as the most prevalent.Most of the babies with CA had passed away when the present study began CA. Kruskal wallis analysis showed a significant difference in mean age of the deceased babies regarding their types of abnormalities (P=0.03). Conclusion: Most of congenital anomalies had a relationship with nervous and cardiovascular systems.Abnormal babies were very prone to death, and frequently they died while being uner one year.Thus,regard to premarital genetic couynseling and undergoing prenatal diagnostic tests are necessary..