Hollow porous fibers containing adhered contaminants are cleaned to remove the contaminants by backflushing a liquid to fill the pores, and adding a flow of gas so as to form a two-phase mixture of gas and bubbles of liquid that can scrub the fibers, loosening the contaminants and allowing them to be flushed from the hollow fibers. The method is particularly useful for cleaning hemodialyzers used for dialysis and hollow fiber modules used in water treatment and separations. The two phase flow method is specifically effective in cleaning piping systems having high length to diameter (l/d) ratios.