To evaluate the diagnostic contribution of the computed tomography (CT) enema and magnetic resonance imaging (MRI) for multifocal (multiple lesions affecting the same segment) and multicentric (multiple lesions affecting several digestive segments) bowel endometriosis. Prospective cohort study (Canadian Task Force classification II-2). Eighty-five patients. Tenon University Hospital, Paris, France. All patients received a preoperative CT enema and underwent MRI interpreted by 2 radiologists. Patients underwent colorectal resection for colorectal endometriosis from February 2009 to November 2012. Nineteen patients (22%) had multifocal lesions, and 11 patients (13%) had multicentric lesions. Six patients (7%) had both multifocal and multicentric lesions. The sensitivity, specificity, and positive and negative likelihood ratios (LRs) of MRI for the diagnosis of multifocal lesions were 0.58, 0.84, 3.55, and 0.5, respectively. The sensitivity, specificity, and positive and negative LRs of the CT enema for the diagnosis of multifocal lesions were 0.64, 0.86, 4.56, and 0.4, respectively. The sensitivity, specificity, and positive LR of MRI for the diagnosis of multicentric lesions were 1, 0.88, and 8.4, respectively. The sensitivity, specificity, and positive and negative LRs of MRI for the diagnosis of multicentric lesions were 0.46, 0.92, 5.6, and 0.59, respectively. No difference was observed between MRI and the CT enema for the diagnosis of multifocal and multicentric colorectal endometriosis. The interobserver agreement was good for MRI and the CT enema (κ = 0.45 and 0.45) for multifocality, and it was poor for both MRI and the CT enema (κ = 0.32 and 0.34) for multicentricity. Both MRI and the CT enema were able to diagnose multifocal and multicentric bowel endometriosis with similar accuracy.