The aim of this study was to evaluate colonoscopy in the diagnosis and treatment of rectal carcinoid tumors with diameter <1 cm. Elevated lesions with normal mucosal appearance under colonoscopy were identified. Endoscopic ultrasound (EUS) was performed in 16 patients. Lesions diagnosed as rectal carcinoid tumors were resected by endoscopic mucosal resection (EMR). The diagnosis of specimens by EMR was confirmed by pathological examination. Immunohistochemical staining was undertaken and follow-up data were collected. Twenty-two lesions were found among the 21 cases. The majority of these were located within 10 cm of the anal opening. Twenty two cases with rectal carcinoids were diagnosed by EUS under colonoscopy and all cases were verified by pathological examination. The resection rate was 95.5% (21/22). Of the lesions, six were mucosal and 10 were submucosal. Immunohistochemistry was undertaken for carcinoid tumors. Histological patterns of rectal carcinoids revealed solid nests or trabecular patterns. Eleven cases were synaptophysin (SYN)-positive, 8 cases were neurone-specific enolase (NSE)-positive and 5 cases were chromogranin A (CgA)-positive. Colonoscopy combined with EUS is effective in the diagnosis and determination of small rectal carcinoids. Endoscopic treatment is effective for small-sized tumors. Pathology and immunohistochemistry remain the diagnostic gold standard.