A device and system for thermally affecting tissue that includes a balloon catheter with a reduced distal length for ease of navigation and that also includes a balloon that is more resistant to bursting and delamination. The balloon may include a proximal neck generally attached to an elongate body and a distal neck generally attached to a shaft disposed within the elongate body. The distal neck is turned inward to extend within the balloon chamber and the proximal neck may either extend within the chamber or extend proximally away from the balloon chamber. Alternatively, the device may include an inner balloon and an outer balloon, the distal necks of both being turned inward and extending within the inner balloon chamber. The proximal necks may both also be turned inward to extend within the chamber or the proximal neck of the outer balloon may extend away from the balloon chamber.
