Background/Purpose: Babies with congenital duodenal obstruction (CDO) have a high incidence of additional anomalies. Downs syndrome (DS) is the most common associated chromosomal defect, affecting up to 20% of these newborns. Morbidity is expected to be higher in DS patients, since it is a major cause of congenital heart disease, immunodeficiency, and other birth defects. We could find only one report concerning the morbidity in the DS newborn, when associated with CDO. The purpose of this report is to compare the postoperative outcome of two groups of newborns with CDO: group I, patients with associated DS and group II, without DS. Methods: A two-center retrospective review of charts of 46 newborns with CDO admitted to the Hospital of “UNICAMP” and the “Hospital das Clinicas da UFMG”, between 1993 and 2001, was undertaken. Results: Sixteen (34,7%) of the 46 babies had DS. The groups were homogeneous concerning gestational age, gender, birth weight and nutritional status. There was a higher incidence of cardiopathy (56% x 20%) and sepsis (37% x 16%) among patients with DS; however we could find statistic difference only for the incidence of cardiopathy. The survival rate was similar for both groups, reaching 94%. Conclusions: Despite the associated anomalies, newborns with DS individuals had a similar postoperative course, when compared with babies without DS after surgical correction of CDO. The earlier diagnosis of CDO and other birth defects, associated with intensive care, appropriate surgical procedure and postoperative support can provide an equivalent morbidity for DS patients.