Background and Aims: Large non-pedunculated rectal polyps are most commonly resected by endoscopic mucosal resection (EMR) or transanal endoscopic microsurgery (TEM). Despite pre-procedural diagnostics, unexpected rectal cancer is incidentally encountered within the resected specimen. This study aimed to compare the diagnostic assessment and procedural characteristics of lesions with and without unexpected submucosal invasion. Methods: A post-hoc analysis of a multicenter randomized trial (TREND study) was performed in which patients with a non-pedunculated rectal polyp of ≥3 cm without endoscopic suspicion of invasive growth were randomized between EMR and TEM. Results: Unexpected rectal cancer was detected in 13% (27/203) of patients; 15 after EMR and 12 after TEM. Most consisted of low-risk T1 cancers (78%, n = 18). There were no differences in the diagnostic assessment between lesions with and without unexpected submucosal invasion. Diagnostic biopsies revealed similar rates of high-grade dysplasia (28% [7/25] vs 18% [26/144]). When compared with EMR of adenomas, EMR procedures of unexpected cancers had a lower success rate of submucosal lifting (60% vs 93%, P <.001), were more often assessed as endoscopically incomplete (33% vs 10%, P =.01), and were more frequently terminated prematurely (60% vs 8%, P =.001). Conclusions: Diagnostic assessment of large non-pedunculated rectal polyps revealed similar characteristics between unexpected cancers and adenomas. Unexpected cancers during EMR were non-lifting in 40%, endoscopically assessed as incomplete in 33%, and terminated prematurely in 60%. In treatment-naive patients, these factors should raise suspicion of malignancy and need discussion in a multidisciplinary team meeting for decision on further treatment strategies.