Our study aimed to assess the diagnostic utility of magnetic resonance enterography (MRE) compared to capsule endoscopy (CE) for the detection of small bowel polyps in patients with Peutz-Jeghers syndrome (PJS); with findings verified by balloon enteroscopy (BE). Adult patients were prospectively recruited across two tertiary centres and underwent MRE followed by CE, with a subsequent BE performed in patients with significant (≥10 mm) polyps. The primary endpoint was the total number of significant (≥10 mm) small bowel polyps detected. The number of patients with at least one significant polyp, correlation with BE findings, and patients' preferences were secondary endpoints. A total of 20 patients (7 male; mean age 34.9 years) underwent both investigations. The number of polyps ≥10 mm detected by CE was greater than by MRE (47 vs 14 polyps, P = 0.02). The number of patients with at least one significant polyp identified by CE was 11 (55 %) compared with 7 (35 %) identified by MRE (P = 0.25). Subsequent BE in 12 patients identified a total of 26 significant polyps in 8 patients. The positive predictive value of finding a polyp at BE was higher for MRE (100 %) compared to CE (60 %). Overall patient preferences identified CE as the preferred modality. This prospective study demonstrated that CE identifies significantly more small bowel polyps compared with MRE in patients with PJS. Correlation between the two techniques and subsequent BE however was relatively poor.