Carotid endarterectomy (CEA) has been shown to be effective in stroke prevention in selected patients. Some studies, however, identified gender as an independent risk factor for perioperative CEA complications demonstrating an increased rate of perioperative stroke or death in women. Furthermore, contralateral internal carotid artery (ICA) occlusion has been associated with higher rates of perioperative CEA complications. Therefore, we sought to analyse the gender-specific risk of perioperative CEA complications between patients with or without contralateral ICA stenosis or occlusion. We retrospectively analysed 212 consecutive CEA patients (male = 156, Female = 56) for their gender-specific, perioperative risk of stroke, transient ischemic attack (TIA), restenosis and cardiac complications in the presence (62%) or absence (38%) of a contralateral ICA stenosis/occlusion. In women but not in men, risk of perioperative ischemic events (stroke, TIA) or re-stenosis (p = 0.036) and combined perioperative complications (ischemic events, re-stenosis or cardiac complications; 38.2 % vs. 9.1%; p = 0.028) was significantly increased in the presence of a contralateral ICA stenosis or occlusion. Furthermore, in the presence of a contralateral ICA stenosis/occlusion the number of perioperative ischemic events (p = 0.008) and combined perioperative complications (38.2 % vs. 14.3%; p = 0.006) was significantly higher in female than in male patients. Our study suggests that women with contralateral ICA stenosis or occlusion may have a significantly higher risk for perioperative CEA complications than other subgroups of CEA patients. This risk increase seems to be gender-specific and, if confirmed in larger prospective studies, may influence ICA stenosis therapy in the presence of a contralateral ICA stenosis/occlusion in female patients.