Various techniques including cold snare polypectomy and endoscopic mucosal resection are used for the removal of small colorectal polyps. Specimens of resected polyps are prepared in pathology laboratories and analyzed to make a pathological diagnosis. However, reports on how different resection methods influence the pathological diagnosis are limited. This article discusses the problems associated with the failure of polyp retrieval and fragmentation of small specimens during collection and the effects of certain parameters on the pathological diagnosis, particularly with regard to surgical margins. In the future, although pathologists are expected to encounter problems as a result of minor findings that are not clinically problematic, relatively rare cases such as submucosal invasion by a small carcinoma should not be overlooked.