Intestinal malrotation is an embryological abnormality modifying the classic anatomy of the small and large bowels, particularly the topographical one. Inflammatory bowel disease (IBD) is characterised by anatomical lesions with preferential intestinal tropism. These two conditions are rarely associated. They represent a real diagnostic and therapeutic challenge due to the overlap of non-specific symptoms and the complexity of the clinical management. We report the case of a young woman presenting with a flare-up of her IBD and a partial common mesentery syndrome. Clinicians should be aware of the potential pitfalls of the two entities to propose the adequate therapeutic strategy regarding the full understanding of the anatomy, notably when surgery is needed.