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Background and study aim A catheter-type endocytoscope has recently been developed that is able to provide in vivo cellular images of gastrointestinal mucosa. Aberrant crypt foci (ACF) represent the earliest precursor of colorectal cancer featuring the dysplasia-carcinoma sequence. The aim of the current study was to assess the potential of the endocytoscopy system (ECS) in the "in vivo" detection of dysplasia in colorectal ACF. Patients and methods Consecutive patients with colorectal ACF were studied with endocytoscopy. Blinded endoscopic and histological assessments were obtained. Lesions were excised en bloc for histology. Results A total of 48 colorectal lesions were examined in 41 patients. The mean duration of the ECS procedure was 44 +/- 12 minutes (range 31 - 62 minutes). The quality of ECS images was rated as good in 39/48, medium in six, and poor in three (6.2 %). It was possible to observe lesions at the cellular level and evaluate both cellular and structural atypia in vivo. In normal mucosa, crypts had preserved individuality and round-shaped contours. Nuclei were located at the basal third of the crypt in a single line, and the lumen was circular. In dysplastic ACF, crypt contours were polygonal, cell nuclei were elongated with pseudostratification toward the luminal half of the crypt and irregularly arranged, and the lumen was linear. In all, 23 endocytoscopic images were labeled as dysplastic and 25 as nondysplastic. Histology confirmed low-grade dysplasia in 21/23 cases (91.4 % sensitivity). Absence of dysplasia was confirmed in the remaining 25 cases (100 % specificity). Interobserver agreement between trained endoscopist and pathologist was good (wK 0.68; 95 % CI 0.59 - 0.78). Conclusions Endocytoscopy provides real-time histological images in vivo, with clear visualization of cellular details and features of dysplasia in colorectal ACF.