The biliary atresia (BA) is the end result of a destructive and idiopathic inflammatory process affecting the intrahepatic and extrahepatic bile ducts, leading to fibrosis and biliary cirrhosis. The objective was to identify factors associated with mortality in children with BA. Observational, longitudinal, analytical and retrospective study carried out in patients with biliary atresia treated between 2008 and 2012 in a tertiary care hospital from the Instituto Mexicano del Seguro Social. A total of 66 patients with BA; 49 were girls (74.2 %), 47 underwent hepatic portoenterostomy (or Kasai procedure: KP), the age at delivery was 4.5 months. When comparing the groups with and without KP, the lower age at the time of delivery, the age of diagnosis, a lower score on the PELD score and the Child-Pugh for the group with Kasai were statistically significant. Patients who died had a PELD score statistically higher (median 20) than those who lived (median 13), p = 0.004. The factor directly related with the mortality was the history of KP with an OR of 0.17 (95 % CI 0.04-0.71, p = 0.016). The prognosis of children with BA remains gloomy because they are diagnosed in late stages. The most important factor associated with mortality in these patients is to perform KP.