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Introduction: Data about the safety of vedolizumab and ustekinumab are lacking in older patients with inflammatory bowel disease. The objective was to compare the safety of vedolizumab and ustekinumab therapies in older patients (>60 years) with inflammatory bowel disease. Methods: This retrospective study included patients with Crohn’s disease or ulcerative colitis initiating vedolizumab, ustekinumab or anti-TNF therapy at >60 years of age. We examined the occurrence of adverse events within one year after therapy. Results: This study included 182 patients: 53 were treated with vedolizumab (22 patients with Crohn’s disease and 31 with ulcerative colitis), 31 with ustekinumab (30 Crohn’s disease and one ulcerative colitis) and 98 with anti-TNF (63 Crohn’s disease and 35 ulcerative colitis). At one year, there was no difference in terms of safety in patients with Crohn’s disease between vedolizumab and ustekinumab considering the number of adverse events per year of follow-up (p = 0.258). For ulcerative colitis and Crohn’s disease, the occurrence of adverse events per year of follow-up was similar between vedolizumab and anti-TNF (p = 0.274 and p = 0.876, respectively). Conclusions: Safety was similar between vedolizumab and ustekinumab in older patients with inflammatory bowel disease.