After surgical management of their oesophageal atresia (OA) and tracheo-oesophageal fistula (TOF), most patients exhibit evidence of gastro-oesophageal reflux (GOR) and many have oesophagitis. However, the aetiology of the GOR is still controversial. This study was undertaken to document whether there are congenital abnormalities in the intra-abdominal oesophagus and the hiatus in the fetal rat with OA and TOF following exposure to adriamycin (ADR). Time-pregnant rats were injected daily with either saline or 2 mg/kg ADR intraperitoneally on gestational days (GD) 6–9. The fetuses (n = 56) from 8 litters were harvested on GD 21 for examination. The length of the oesophagus between the diaphragmatic crura and the gastro-oesophageal junction (GOJ) and the sizes of the stomach and the oesophageal hiatus were measured under a dissecting microscope. The length of the oesophagus between the diaphragmatic crura and the GOJ in the ADR-treated fetuses (0.85 ± 0.37 mm) was significantly shorter than in control fetuses (2.41 ± 0.32 mm) (P < 0.0001). The size of the stomach in ADR-treated fetuses (5.30 ± 1.01 mm) was significantly smaller than in the controls (8.07 ± 0.49 mm) (P < 0.001). Moreover, the size of the oesophageal hiatus in ADR-treated fetuses (1.16 ± 0.43 mm) was markedly larger than in the controls (0.32 ± 0.1 mm) (P < 0.0001). These results showed that the congenital abnormalities in ADR-treated rat fetuses may account for the oesophageal functional disorders seen after surgical correction in patients who have OA and TOF.