Little is known about real-time in-vivo microscopy of pulmonary capillary perfusion because current microscopy requires direct access to lung tissue with surgical intervention such as the thoracic-window technique and open-lung model. To evaluate if probe-based confocal laser scanning endomicroscopy (pCLE) via the trachea allows for real-time in-vivo visualisation of pulmonary capillary density and red blood cell (RBC) velocity in pigs. An interventional animal study. European University Hospital. Nine female domestic pigs (50 to 60 kg) were used. A pCLE probe was positioned in non-dependent, central and dependent lung zones in nine anaesthetised pigs (Alveoflex, Cellvizio, Maunakea, France). After intravenous administration of fluorescein isothiocyanate dextran as contrast agent repetitive pCLE videos were recorded during pressure-controlled ventilation (PCV) or continuous positive airway pressure for 3 min each. Using fluorescein isothiocyanate-labelled RBC erythrocyte velocities in pulmonary capillaries were quantified. Data are expressed as mean ± SD or median with interquartile range (IQR). Capillary density was greater in dependent and central as compared with non-dependent lung zones [[32 (29 to 34) %] and 32 (30 to 34) % vs. 28 (26 to 28) %, respectively, P < 0.05]. During PCV, RBC velocities were higher in larger lung capillaries [diameter >20 μm, 309 μm s(-1) (209 to 397)] than intermediate [diameter 10.1 to 20 μm, 146 μm s(-1) (118 to 235)] and small [diameter <10 μm, 153 μm s(-1) (117 to 236), P < .05]. During continuous positive airway pressure of 1.5 kPa, RBC velocities in dependent lung areas decreased to 47 μm s(-1) (30 to 82) compared with 198 μm s(-1) (148 to 290) during PCV (P < 0.05). pCLE allows endoscopic real-time in-vivo imaging of pulmonary capillary morphology and perfusion. Alterations in pulmonary capillary blood flow induced by different ventilator regimens can be detected. This minimally invasive approach via the endotracheal route is feasible in an experimental setting and may help to understand changes in regional pulmonary capillary perfusion.