Congenital diaphragmatic hernia (CDH) is a rare condition. The aetiology of CDH is often unclear. In our case, a hollow mass was noted on MRI. Cardiac ejection fraction was diminished (47.0%) compared to 60.5% (average of 10 other normal animals, P < 0.05). The final diagnosis of congenital diaphragmatic hernia (Bochdalek type) was made when the sheep underwent surgery. The hernia was right-sided and contained the abomasum. Lung biopsy demonstrated incomplete development with a low number of bronchopulmonary segments and vessels. The likely cause of this hernia was genetic malformation.