OBJECTIVE: To measure the oxidant/antioxidant status of newborn babies with oesophageal atresia and their mothers, compared with healthy control subjects. METHODS: This case control study included 40 participants: 10 newborns with oesophageal atresia and their mothers, and 10 healthy newborns and their mothers. Whole blood malondialdehyde (MDA) levels and the activities of antioxidant enzymes (catalase, carbonic anhydrase [CA], glucose-6-phosphate dehydrogenase [G-6-PD], and superoxide dismutase [SOD]) were measured. RESULTS: MDA levels and CA activity were significantly higher, and catalase, SOD and G-6-PD activities were significantly lower, in newborns with oesophageal atresia and their mothers than in healthy newborns and their mothers. Although CA activity was similar between the newborns and mothers in the patient group, it was significantly lower in newborns than in mothers in the healthy group. CONCLUSIONS: Increased lipid peroxidation might play an important role in the pathogenesis of oesophageal atresia. Impairment of the free radical/antioxidant balance may lead to increased free radical and decreased antioxidant levels in oesophageal atresia.