<b><i>Objectives:</i></b> This open label, phase I clinical trial (NCT02945462) using 2 consecutive intracavernous autologous bone marrow-derived mesenchymal stem cells (BM-MSCs) for the first time in the treatment of diabetic patients with erectile dysfunction (ED). The primary outcome is to assess the safety and tolerability of intracavernous autologous BM-MSCs, the secondary outcome is to assess efficacy of the procedure. <b><i>Patients and Methods:</i></b> Four diabetic patients with refractory ED were included. Two consecutive intracavernous autologous BM-MSC injections were performed. Tolerability was assessed immediately and at 24 h, safety was evaluated for 2 years. Efficacy was assessed using International Index of Erectile Function-15 (IIEF-15) and Erection Hardness Score (EHS) for 12 months. <b><i>Results:</i></b> procedure was well tolerated and no patients reported significant adverse effects. There was significant improvement of IIEF-15 and EHS; IIEF-15 (<i>p</i> = 0.04), Erectile Function (<i>p</i> = 0.03), Sexual Desire (<i>p</i> = 0.04), Intercourse Satisfaction (<i>p</i> = 0.04), and Overall Satisfaction (<i>p</i> = 0.04). <b><i>Conclusion:</i></b> This is the first human study with proven tolerability, safety and efficacy of intracavernous autologous BM-MSC injections for treatment of diabetic patients with ED.