Background ABO blood group system has been clinically related to an increased incidence of cardiovascular diseases. Preliminary data relating Rhesus (Rh) factor and these outcomes also have been published. Our aim was to analyse the impact of blood group on the short and long-term outcomes after carotid endarterectomy (CEA). Materials and methods From 2012 to 2019, patients from a referral centre who underwent CEA for atherosclerotic carotid stenosis were prospectively followed. Our primary outcomes were long-term major adverse cardiovascular events (MACEs) and all-cause mortality. Secondary outcomes were perioperative complications and myocardial injury after non-cardiac surgery (MINS). Median follow-up was 50 months (interquartile range 21–69). Time-to-event analysis was used to determine the effect of ABO and Rh groups in long-term outcomes. Results One hundred and eighty-four patients were included, with a mean age of 70.1 ± 9.1 years. Eighteen (25.7%) patients with O type and 48 (42.1%) patients with non-O type presented coronary artery disease (odds ratio [OR]: 2.313, 5–95% confidence interval (CI) 1.245–4.297, p = .008). Patients Rh+ presented significantly more congestive heart failure, 23 (14.7%), p = .03. The incidence of MACE in the long-term was higher in non-O patients (adjusted hazard ratio: 2.034; CI: 1.032–4.010, p = .040). Rh− patients, presented a higher incidence of perioperative MINS. However, there was no statistically significant association with long-term risk of MACE. Conclusion The incidence of MACE in long-term analysis was higher in non-O blood type and 30-day MINS was significantly more common amongst Rh− patients. The benefit from a more complete preoperative cardiac study in these patients should be performed.