Despite great advancements in therapy, it remains unclear why inflammation in the digestive system of patients suffering Crohn’s Disease (CD) is progressive and leads to complications (e.g., enteric fistulas) that are only alleviated by surgical removal of the damaged bowel. By using a three-dimensional profiling method, we recently discovered that surgically removed CD bowels have complex 3D-networks of microscopic lesions that follow principles of ‘geological caverns’. Because such lesions contain purulent debris (pus), inflammatory cells, and bacterial DNA, their collective presence with that of bacteria could explain CD progression and recurrence.