Abstract Background The natural history of intestinal lesions in Crohn’s disease [CD] is not fully understood. Although the extent of lesions at diagnosis usually defines the extent of the disease, some lesions seen at diagnosis, particularly aphthous ulcers [AUs], may resolve before follow-up. The aim of this study was to evaluate the outcomes of CD patients with colonic AUs seen at diagnosis. Methods CD patients with aphthous colitis at diagnosis who had been followed since 2001 were included in a case control study matched with two groups of controls: one without colonic involvement at diagnosis and a second group with colonic lesions more severe than AUs at diagnosis. Results Seventy-five patients were included, with a median follow-up of 7.3 years [interquartile range 2.7–9.8]. Seventy-one per cent of those having a second colonoscopy at least 6 months after diagnosis were stable or healed. Medical treatments were similar between the three groups. The AU group’s rate of ileal surgery was similar to those without colitis. In multivariate analysis, the independent factors associated with ileal resection were ileal involvement (odds ratio [OR]: 8.8; 95% confidence interval [CI] [7.68–33.75]; p = 0.002) and the presence of severe colitis (OR = 0.5; 95% CI [0.32–0.79], p = 0.003). The risk of ileal surgery was not influenced by the presence of aphthous colitis (OR: 0.63; 95% CI [0.37–1.1]; p = 0.1). Conclusion Aphthous colitis at diagnosis seems to resolve in most patients. This suggests that these lesions are of little clinical significance and may not need to be considered prior to ileal resection in CD or when making other important therapeutic decisions.