Background: Several studies have reported that right-sided colon cancers (RCC) and left-sided colon cancers (LCC) differ in several factors including genetic features. We investigated the difference in clinicopathological characteristics and oncogenic mutation status between patients with RCC and LCC in all stages. Methods: This study was a prospective, observational study. Patients were recruited from December 2014 to February 2016. Formalin-fixed paraffin-embedded tissue blocks were collected and DNA wes extracted from tissue sections from 158 cases. Mutations in KRAS, NRAS, HRAS, BRAF and PIK3CAwere detected by next-generation DNA sequencer. Tumors from cecum to transverse colon were defined as RCC, and tumors from descending colon to rectsigmoid were defined as LCC. Results: RCC was 66 patients and LCC was 92 patients. Poorly differentiated adenocarcinoma or mutinous adenocarcinoma were significantly more frequent in RCC compared to LCC (P = 0.047). KRAS mutations were detected in 35 patients with RCC (53.0%) and in 32 patients with LCC (34.8%). NRAS mutations were detected in 2 patients with RCC (3.0%) and in 3 patients with LCC (3.3%). There was no HRAS mutation in all patients. BRAF mutations were detected in 7 patient with RCC (10.6%) and in 2 patients with LCC (2.2%). PIK3CA mutations were detected in 8 patients with RCC (12.1%) and in 10 patients with LCC (10.9%). KRAS and BRAF mutation in RCC were significantly more frequent than in LCC (P = 0.022 and P = 0.024, respectively). These mutations were not significantly different according to tumor stage. In this study, both KRAS and BRAFmutations were exclusive. Conclusions:KRAS and BRAF mutation were more frequent in the patients with RCC compared to those with LCC in all stages. This study suggested that it was important to evaluate BRAF mutation in addition to KRAS in order to select more effective treatments, especially in RCC.