Purpose: The purpose of this study was to evaluate the prevalence and the underreporting rate of sacroiliitis (SI) in a large cohort of patients with biopsy-proved Crohn’s disease (CD) who underwent magnetic resonance enterography (MRE) or computed tomography enterography (CTE). Materials and Methods: Patients with CD were recruited from eight Italian health centers in the period from January 2013 to December 2017. Disease activity was recorded according to the CD activity index (CDAI). The scans were read by two blinded readers who defined the presence of SI according to Assessment of SpondyloArthritis International Society (ASAS) classifications and European League Against Rheumatism (EULAR) recommendations. Moreover, SI was scored using a simplified Spondyloarthritis Research Consortium of Canada (SPARCC) scoring system. Results: Interobserver agreement in diagnosing SI on imaging was good (K = 0.72–0.83). SI was diagnosed in 129 (14.4%, 54 men, 75 women) out of 894 patients; however, sacroiliac joint (SIJ) abnormalities were not mentioned in the radiological reports of 112 patients (86%). Fifty (38.7%) out of 129 patients also underwent a subsequent SIJ evaluation through a dedicated MRI protocol to confirm SI. SI was found in a higher percentage of patients with “active” than “inactive” CD (18% vs. 4%). Conclusion: This study confirms the feasibility of CTE and MRE for the screening of SI in CD patients; however, it also underlines the remarkable problem concerning the underreporting of this entity in radiological practice.