Previous studies have linked apical periodontitis (AP) to inflammatory bowel disease (IBD). The aim of this study was to compare the prevalence of AP and root canal treatment (RCT) in patients with ulcerative colitis (UC) and Crohn´s disease (CD). A cross-sectional study, including 28 patients with Crohn´s disease and 26 with ulcerative colitis, was conducted. AP was diagnosed as radiolucent periapical lesions (RPLs), using the periapical index score (PAI). Student?s t test, 2 test and multivariate logistic regression were used in the statistical analysis. Multivariate logistic regression run with age, gender, number of teeth, number of RFT, periodontal disease and the type of IBD as covariates, taking as dependent variable and outcome ?periapical status? (0 = no tooth with RPL; 1 = at least one tooth with RPL), showed that both UC and CD patients had the prevalence apical periodontitis (OR = 1.03; C.I. 95% = 0.25 ? 4.31; p = 0.97). The multivariate analysis, including all the above covariates, shows that both in UC and CD patients the prevalence of RCT was similar (OR = 0.76; C.I. 95% = 0.17 ? 7.31; p = 0.73). Periapical status was significantly associated with endodontic status (OR = 42.72; C.I. 95% = 3.87 ? 472.15; p = 0.002), regardless of IBD type. The results of the present study show similar frequency of AP and RFT in both UC and CD patients. The type of IBD does not appear to affect the prevalence of radiographically detectable periapical lesions or the prevalence of root canal treatment.