A catheter system for treating pulmonary emboli has an multi-channel access port for establishing and maintaining communication with the vascular system and provide guidance for endovascular catheterization. One catheter may traverse the port and extend through the heart to the pulmonary arteries to inject lysing agents, contrast media, medicaments and to remove blood clots. Another catheter may traverse the port and extend through the vena cava to other parts of the venous tree to supply the same agents and to remove blood clots there. A third catheter may telescope over the treatment catheter through the vena cava and occlude the affected vein. Gas pervious tubules on the third catheter provide oxygen enrichment of the venous blood.