A seal is provided for effectively inhibiting the egress of fluids from the working channel of an endoscope when an elongate device having a region with a non-circular cross-sectional shape is disposed therein. The seal has a body portion with a proximal end adapted for insertion of the elongate device, a distal end adapted for connection to the proximal end of the endoscope, and a wall defining a lumen adapted to receive the elongate device and to provide access to the working channel of the endoscope. The seal includes a sealing element for sealing the region of the elongate device with a non-circular cross-sectional shape. The sealing element conforms to the profile of the non-circular region.