Abstract Background Sexual dysfunction is often associated with impaired body image and quality of life in patients. However, little data exists on sexual dysfunction (SD) in patients with Chronic Inflammatory Bowel Disease (IBD). The aim of this study was to assess the prevalence and risk factors for sexual dysfunction in patients with IBD. Methods This is a cross-sectional study of all patients followed for IBD. Sexual function was assessed by the Female Sexual Index Function (FSIF) for women and the International Index of Erectile Function (IIEF) for men. Sexual dysfunction was confirmed when the total FSIF score was less than 26, or the IIEF score less than 26. Crohn’s disease (CD) activity was assessed by the Harvey-Bradshaw index (HBI), and that of ulcerative colitis (UC), by the clinical Mayo scores. Results We collected 100 patients, with a mean age of 42.18 ± 15.71 and a sex ratio (M / F) = 1.5. Sixty eight patients had CD and 32 patients had UC. Ano-perineal manifestations were present in 38.2% of cases. Severe disease activity was noted in 14 patients (20.6%) with CD and 10 patients (31.3%) with UC. Twelve patients had proctitis. 38% of patients had surgical treatment: 18.75% for patients with UC and 47.05% for those with CD. Total colectomy was performed in 12% of cases. At the time of the study, 20% of patients were on systemic corticosteroid therapy, 22% on Azathioprine, 4% on Salazopyrine, 8% on 5-ASA and 46% on Anti-TNFα. Sexual dysfunction was reported by 42.9% of women: 57.14% (UC) vs 38.46% (CD) (p = 0.042). On the other hand, sexual dysfunction was reported by 27.6% of men: 22.2% of men with UC and 28.57% with CD, with no statistically significant difference (p = 0.78). A significant association was found between sexual dysfunction and the degree of disease activity (p <0.001 for CD, p = 0.003 for UC), as well as pancolitic involvement in women with UC (p = 0.002). However, the presence of anoperineal manifestations, rectal involvement and history of surgery were not significantly associated with the frequency of sexual disturbances. Conclusion Our study showed a high prevalence of sexual dysfunction in patients with IBD. Training gastroenterologists in the management of sexual dysfunction would make it possible to satisfy patient expectations.