Background Colon cancer is a common malignant tumor in the clinic with an incidence rate that is increasing in recent years. The key point for improving the survival rate is the diagnosis and treatment at an early stage. The purpose of this study was to compare the difference of the Fuji Intelligent Chromo Endoscopy (FICE) and staining technique for the diagnosis of colon tumors and non-tumor lesions.Methods From March to November 2007, 654 patients were examined with ordinary colonoscopy. Among them 223 patients with colon neoplasm or polypoid lesion were included. The patients were examined with a magnifying ordinary colonoscopy, a magnifying FICE technique and magnifying staining technique. The pit pattern and blood capillary form of the lesion were examined, an endoscopic diagnosis was made and it was compared with the pathologic diagnosis.Results Four hundred and fifty-one neoplasms were detected in the 223 patients, among those 91.1% (411/451) were detected with the magnifying ordinary endoscopy while 99.1% (447/451) were detected with the FICE technique; there was a significant difference between the two methods. FICE could clearly show the structure and form of mucosal blood capillaries (P＜0.01) but there was no significant difference between the two methods for showing the pit pattern. The coincident rate of FICE for the diagnosis of tumor and non-tumor lesions was 91.6% (413/451), that of the magnifying staining technique was 82.0% (370/451) (P＜0.05).Conclusions Magnifying FICE could show the mucosal microstructure and blood capillary form and it had a superiority of high coincident rate, high sensitivity and specificity when compared with ordinary magnifying colonoscopy and magnifying staining endoscopy. In addition, it was easy to operate and a biopsy could be taken from the target, so it has a satisfactory clinical practical value.