Background Management of malignant rectal polyps (MRPs) after endoscopic polypectomy (EP) is still debated. It is sometimes difficult to decide whether to simply follow-up (FU) or to treat such a removed lesion. Transanal endoscopic microsurgery (TEM) could have a role both in T staging and in treating MRPs after EP. Methods Patients who underwent a full-thickness TEM within 3 months after an EP between January 2008 and October 2012 were retrospectively analyzed. If post-TEM histology showed locally advanced rectal cancer, patients underwent a total mesorectal excision (TME) within 4-6 weeks. Patients without malignant disease or pT1sm1 cancers at post-TEM histology were followed up every 3 months for 2 years with clinical examination, flexible rectal endoscopy, and neoplastic markers monitoring. Results A total of 39 patients were included. Post-EP histology was adenocarcinoma in 27/39 cases (69.2 %) and adenoma in 12/39. Mean operative time was 64.2 min; no 30-day mortality occurred; 30-day morbidity was 2.7 % (rectal bleeding in 1/39 cases). Post-TEM histology showed a T2 cancer in 5/39 patients, four with and one without a previous cancer diagnosis, who were further treated by TME (four RARs and one APR) and are disease free with a mean FU of 24.2 months. Post-TEM histology showed adenoma in 10/39 cases and fibrosis in 24/39. These patients are disease free with a mean FU of 13 months. Conclusions A full-thickness TEM after EP of MRPs can establish the presence of residual malignant disease and its depth of invasion, precisely defining the indication to TME. In event of benign post-EP histology, TEM must be performed in presence of macroscopic residual disease, in order to obtain an RO resection and finally exclude cancer, while, in absence of macroscopic residual disease, only close FU is required. Keywords Rectal polyps Endoscopic mucosal resection Transanal endoscopic microsurgery Total mesorectal excision Colorectal cancer (CRC) represents the most frequently diagnosed neoplasm in Europe (436,000 new cases/year, i.e. 13.6 % of diagnosed tumors) [1] and accounts for 8 % of deaths for neoplasm in the world and 12.2 % in Europe [2]. With