Transanal total mesorectal excision (TaTME) is an alternative technique for rectal surgery that could facilitate the mobilization and the distal transection of the rectum. Our objective was to analyze whether the presence of factors affecting the difficulty of laparoscopic total mesorectal excision (TME) could affect surgical and oncological outcomes of TaTME for mid and low rectal cancer. 20 patients (13 male, 7 female) with a mean age of 66.5 years (range 55.5–75.7) and mid–low rectal cancer were prospectively submitted to TaTME. Every TaTME procedure was performed by two teams of experienced surgeons working simultaneously. Adverse conditions for laparoscopic TME were considered to be male gender, obesity, benign prostatic hypertrophy, low rectal cancer, pT3-T4, tumor size >5 cm, and neoadjuvant therapy. These factors were matched to surgical (morbidity, operative time, conversion rate) and pathological (quality of mesorectum, circumferential resection margin) outcomes. Male gender was associated with longer operative time (285 vs. 240 min, p = 0.031). There were no significant associations among the rest of the analyzed factors complicating laparoscopic TME and pathological and surgical outcomes of TaTME. Multivariate analysis showed that male gender was independently associated with operative time (β = 0.18 OR 1.019 CI95%:1.001–1.037; p = 0.042). TaTME seems to be more difficult in males but not in obesity, benign prostatic hypertrophy, low rectal cancer, pT3-T4, tumor size >5 cm, or neoadjuvant therapy. TaTME could be considered an alternative surgery for low rectal cancer in the presence of these factors affecting laparoscopic TME.