Differentiation between rectal and sigmoid carcinomas is a diagnostic challenge with important implications for further treatment. Depending on the tumor stage, treatment for rectal carcinoma consists of preoperative (chemo)radiotherapy and surgery. Sigmoid carcinomas are treated with surgery alone. We established the diagnostic accuracy of flexible endoscopy, MRI and/or CT scan, and both modalities combined as reflected by the conclusion of our multidisciplinary team (MDT). Furthermore, we assessed the treatment consequences of misdiagnosis. Consecutive patients were included who underwent surgery from January 2012 to January 2017 for colorectal carcinoma located ≤20 cm from the anal verge as determined by flexible colonoscopy. Diagnostic accuracy of MRI/CT, flexible endoscopy and the final MDT conclusion were analyzed as index test. The location of the tumor during surgery and the type of surgery was the reference standard. We included 293 patients. Flexible endoscopy had a diagnostic accuracy of 90% and for MRI/CT scanning this was 86–87%. Combination of both modalities improved diagnostic accuracy to 96%. Due to misdiagnosis during initial staging, three patients (1%) erroneously underwent neoadjuvant treatment and in two patients neoadjuvant treatment was potentially erroneously omitted. In conclusion, the combination of both flexible endoscopy and MRI/CT (the MDT conclusion) improves diagnostic accuracy. Erroneous clinical diagnosis can lead to under- and overtreatment.