Abstract Background Local injection of adipose tissue-derived mesenchymal stem cells [MSCs] is effective in fistulizing perianal Crohn’s disease [CD]. Less is known about bone marrow-derived MSCs and little is known about predictive factors of response and magnetic resonance imaging [MRI] evolution of the fistulae after MSC injection. Our aims were to evaluate the safety and clinical outcome of bone marrow-derived MSC injection for perianal fistulizing CD, to evaluate the MRI evolution of the fistulae and to identify factors associated with fistula closure. Patients and methods All CD patients with perianal fistula and appropriate drainage with a seton without abscess at MRI were eligible. Clinical examination, biomarkers and pelvic MRI were performed at weeks 0, 12 and 48. The clinical outcome was assessed by closure of the treated external openings at clinical examination and MRI exploration. Results Sixteen patients with a median age of 49 years and a median duration of perianal CD of 8 months were included. No unexpected safety event occurred. At weeks 12 and 48, 9/16 and 8/16 patients had complete fistula[e] closure, respectively, whereas 11/16 patients had at least partial closure. At MRI, the degree of fibrosis increased significantly after MSC injection. In total, 86% of patients with >80% of fibrosis of the fistula tract at week 48 had fistula closure. Fistula closure at week 12 was predictive of fistula closure at week 48. The MAGNIFI-CD did not change significantly over time. Conclusion Open-label injection of bone marrow-derived MSCs was safe and was effective in half of the patients in fistulizing perianal CD and induced significant MRI changes associated with favourable clinical outcome.