Apparatus for sheathing an endoscopic tool includes a sheathing assembly, which includes a sleeve dispenser and a port adapter for mating with a proximal port of an endoscopic working channel so as to permit the endoscopic tool to be advanced through the sheathing assembly into the working channel. A flexible sleeve in the sheathing assembly has a distal end, which is fixed to the sleeve dispenser, and a proximal end, which is adapted to engage the endoscopic tool as the endoscopic tool is retracted from the working channel, causing the sleeve to extend out of the dispenser in a proximal direction so as to sheath the endoscopic tool.