CAS has emerged as an alternative to carotid endarterectomy for the treatment of significant carotid artery stenosis. We investigated if the side of the stenosis treated has an influence on the neurological outcome of our patients. CAS was performed in 1124 patients at our center. The left carotid artery (group L) was intervened in 557 and the right carotid artery (group R) in 567 patients. Data of both patient groups were analyzed with respect to the total rate of peri-interventional ischemic cerebral events, defined as transient ischemic attacks, minor and major strokes, respectively. The total peri-interventional ischemic cerebral event rate was 10.1% in group L and 6.7% in group R (p = 0.042), respectively. The routine use of a filter wire resulted in a significant reduction of complication rates in group L (from 14.7 to 7.1%; p = 0.005) but not in group R (from 7.8 to 6.0%; p = 0.505). Ischemic cerebral events did not differ between group L and R, when only patients in whom a filter wire was used were analyzed (7.1% in group L and 6.0% in group R, p = 0.174). Peri-interventional ischemic cerebral complication rates in patients undergoing CAS differ with respect to the side treated. This may be due to a more frequent plaque mobilization caused by the guiding catheter.