Objective: To evaluate the neonatal morbidity due to congenital malformations in the city of Petrolina-PE, from 2008 to 2013. Methods: A descriptive study with data from the Information System on Live Births (Sinasc). The analyzes were carried out through frequency distribution and measures of central tendency and dispersion. The associations were tested by the Pearson and Kruskal Wallis chi-square tests. Significance was set at 5% and 95% confidence. Results: 436 cases of congenital malformations were recorded in the study period, with 2011 being the highest occurrence year. The mothers of the newborns were young (25.2 years old), single, upper level of education and household. In general multiparous, with single gestation, vaginal delivery and performed up to six prenatal visits. The newborns were males, at 39 weeks or more of gestation and with normal weight (> = 2500g). The malformations of the musculoskeletal system were the most frequent followed by the genitourinary system. Congenital malformations were especially associated with neonatal characteristics such as gender and weight. In all causes the mean weight was greater than 2500g (p <0.05). The causes of malformation of greater occurrence in both sexes were osteomuscular (p <0.05). The aspects of the mother did not present significant differences in the present study (p> 0.05). Conclusion: The present study evidenced relevant aspects in the occurrence of morbidities due to congenital malformations, directing to a greater attention the occurrence of these diseases especially in relation to the newborn.