A catheter system is described for performing protected angioplasty and stenting of a patient's carotid bifurcation. A self-expanding stent is deployed across a stenosis in the patient's carotid artery. A catheter system that includes a rapid exchange angioplasty catheter with an occlusion balloon catheter positioned through the guidewire lumen is advanced through the guiding catheter to the distal end of the stent. A releasable linking device holds the catheter system together as a unit. The occlusion balloon is inflated within the stent to occlude the carotid artery and to prevent any embolic debris from traveling downstream from the treatment site. The angioplasty balloon is inflated to dilate the stenosis and to complete the expansion of the stent. The angioplasty catheter is withdrawn and any potential embolic debris is aspirated out through the lumen of the guiding catheter. The occlusion balloon is deflated and the catheter system is withdrawn.