Congenital diaphragmatic hernia (CDH) is a congenital anomaly characterized by a defect in the diaphragm. Despite the recent improvements in its treatment, CDH is associated with a high rate of neonatal mortality, which is often related to pulmonary hypoplasia (PH) as well as pulmonary hypertension. A better understanding of the underlying pathological mechanisms of PH in CDH could help establish a new treatment to improve its prognosis. In this study, we investigated serum biological profiles in neonates with CDH. For comprehensive investigation, umbilical cord serum samples were collected from isolated CDH cases (n = 4) and matched healthy controls (n = 4). Samples were analyzed using liquid chromatography-tandem mass spectrometry. A total of 697 proteins were detected; of them, 98 were identified as differentially expressed proteins. Among these differentially expressed proteins, complement C1q subcomponent showed the largest fold change, followed by complement C5. In the pathway enrichment analysis, the complement and coagulation cascades expressed the most significant enrichment (p = 2.4 × 10-26). Thus, the complement pathway might play some role in the pathophysiology of CDH.