Congenital malformations occur due to genetic, environmental, and mixed factors or unknown causes. This study aimed to investigate the existence of a relationship between the type of congenital malformation and maternal and neonatal variables. This prospective, quantitative study was conducted in three public neonatal units in Fortaleza, Ceará, Brazil. Data were collected from the medical records of 159 malformed neonates and analyzed using the Chi-square test (χ2), significance level of 5% (p<0.05). The majority of the newborns were male, 85 (53%), 91 (57%) born full-term, and 82 (52%) weighed between 2500g and 3999g. Malformations of the central nervous and musculoskeletal systems exceeded the other categories. Variables such as gender, gestational age, birth weight, drug use, maternal age, family income, education level, and number of children showed statistically significant associations with the categories of malformations (p<0.05). Maternal and neonatal factors have close relationships with the type of malformation, with these data providing support for neonatal nursing care.