Background and study aims Probe-based confocal laser endomicroscopy (pCLE) enables real-time optical biopsy. Little is known about pCLE imaging deep inside the small bowel, therefore the aim of this study was to determine its usefulness. Patients and methods Between April 2014 and January 2016, we performed 38 pCLE examinations during double-balloon enteroscopy with intravenous fluorescein in 37 patients with: tumors (n = 10), vascular disorders (n = 6), inflammatory diseases and drug injuries (n = 13), other disorders (n = 4), and normal findings (n = 4). We measured the calibers of capillary and lymphatic vessels at 15 different sites and compared the calibers between pCLE images and histopathology. We also compared pCLE findings with pathologic diagnosis. Results The inner diameters of capillary vessels beneath the epithelium and in the middle of villi were 16.2 ± 3.0 µm and 14.5 ± 3.1 µm, respectively, in the pCLE images, but these were not consistent with formalin-fixed paraffin-embedded histology. In tumors, larger capillary vessels were observed in aggressive malignant lymphoma and metastasis, and a “soccer ball-like pattern” constituting homogenous dark cells packed with polygonal, narrower capillary vessels was characteristic in pCLE images of a malignant lymphoma follicle. Hereditary hemorrhagic telangiectasia and angiodysplasia contained anastomosis of capillary vessels of different calibers. In IgA vasculitis, segmental capillary strictures were observed. Intestinal lymphangiectasia with protein-losing enteropathy contained a reticular network of lymphatic vessels and dilated lymphatic ducts accompanied by numerous cell gaps. pCLE findings corresponded to pathologic diagnosis in 32 examinations (91 %). Conclusions pCLE is useful for in vivo analysis of abnormalities of the capillary and lymphatic vessels and epithelium, and for diagnosis in various small-bowel diseases.