A system for performing a medical treatment in a blood vessel while providing downstream microcirculatory system protection, the system being composed of: a catheter having a longitudinal axis, a distal end, an outer lateral surface, a central blood bypass flow lumen extending along the longitudinal axis and opening at the distal end, blood flow inlet and outlet openings extending from the lateral surface and communicating with the bypass flow lumen, and first and second inflation lumens extending to the lateral surface at respective first and second locations that are spaced apart along the longitudinal axis and that are between the inlet openings and the outlet openings; and first and second inflatable members secured to the lateral surface and each having an interior that communicates with a respective one of the first and second inflation lumens, wherein the catheter has a thin outer wall enclosing a hollow interior that is completely occupied by the bypass flow lumen, except for the space occupied by the first and second inflation lumens.