Purpose <p>The surgical treatment of perianal fistulas is challenging, especially in complex cases. Many surgical options may cause impairment of the anal sphincter with subsequent incontinence or may be less effective with a high number of relapses or the persistence of the pathology. New techniques, such as the use of mesenchymal stem cells, are becoming increasingly important because of their effectiveness and lower risk of complications.</p> Methods <p>In this single-centre prospective observational study, patients with complex perianal fistulas were treated via the infiltration of mesenchymal stem cells that had been purified using the Lipogems® system.</p> Results <p>This study included 63 patients with complex perianal fistulas who were treated with mesenchymal stem cells extracted from adipose tissue. Successful clinical healing was observed in 43 (68.25%) patients. Eleven (17.4%) patients presented recurrence after treatment, and 9 (14.3%) had persistent incomplete healing. Minor postoperative complications were observed in six (9.5%) patients, which were related to adipose tissue harvesting in three patients. In the majority of patients, postoperative pain was mild or not present.</p> Conclusions <p>Mesenchymal stem cells offer an innovative therapeutic tool for treating perianal fistulas. This study confirms their safety and efficacy in treating complex perianal fistulas. Nevertheless, more extensive patient follow-up is necessary, as demonstrated by the most recent literature on related techniques.</p>