The present invention heat exchanger with extruded multi-chamber manifolds (16,18) includes at least two panels (22), with each panel having a row of at least one channel which communicates fluid. The heat exchanger includes a first manifold and a second manifold, the first manifold and the second manifold each having at least two manifold chambers (20). Each panel is attached to a manifold chamber of the first manifold and a manifold chamber of the second manifold, with each chamber having an inner wall (40) and outer wall (42). The outer wall has a surface (56) exposed outside the manifold chambers. There is also an opening (62) through the outer wall including a bypass slot. The bypass slot allows fluid communication between the chambers.