A newly developed autofluorescence (AF) imaging technique was applied during colonoscopy in a clinical setting. This pilot study was conducted to evaluate the clinical feasibility of applying AF endoscopy for distinguishing colorectal lesions. A total of 54 colorectal mucosal lesions obtained from 43 patients who underwent both white-light and AF endoscopy and were treated by endoscopy or surgery were assessed. Of the lesions, 11 were hyperplastic polyps, 30 were adenomas and 13 were carcinomas. To quantify the AF intensity, a color-contrast index (CCI) was determined and evaluated in relation to the histology, size and shape of each lesion. CCI was significantly associated with the histology and size of the lesions, but not their shape. CCI increased as the malignant potential increased (in the order of hyperplastic polyps→adenomas→carcinomas), irrespective of the lesion size (r=0.797, p<0.0001 for size>8 mm; r=0.622, p=0.0045 for size>8 mm but >15 mm; r=0.644, p=0.0071 for size>15 mm). In each size group, CCI tended to be higher for carcinomas than for adenomas, and also higher for adenomas than for hyperplastic polyps. CCI allowed discrimination of adenomas/carcinomas from hyperplastic polyps with 95.3% sensitivity and 63.6% specificity (cut-off value, 14.5), and of colorectal carcinomas from adenomas with 84.6% sensitivity and 80.0% specificity (cut-off value, 28.0). These results suggest that the quantitative analysis of AF intensity using CCI is helpful to discriminate among different types of colorectal mucosal lesions, including carcinomas.