A unique clinical case of a combination of malformations of the anterior abdominal wall (omphalocele of large size) and malformation of the lymphatic system (congenital chyloperitoneum) is presented. Each of these defects can lead to a fatal outcome, and the combination of them has greatly increased the risk of developing an unfavourable outcome. The use of immunosuppressive therapy with Sirolimus used for the first time during the newborn period made it possible to completely stop the chyloperitoneum. This clinical example shows that in the treatment of surgical patients with multiple congenital malformations, a multidisciplinary approach and observation is necessary for timely response to the patient’s condition.