OBJECTIVES: Stenting of the arteria carotis interna (CAS) is becoming an increasingly popular means of treating carotid stenosis. At present however costs of stents are high and conclusive trials to prove the (equal) effectiveness of CAS as compared to carotid endarterectomy (CEA) are not finalized yet. The primary goal of the current study is to assess the uncertainties concerning long- and short-term clinical outcomes on the cost-effectiveness analysis of CAS verses CAE. METHODS: A Markov model was constructed to assess the cost-effectiveness for carotid treatment for the Dutch setting based on clinical data published in literature and in-house collected cost data. RESULTS: The procedural costs for the CAS procedure are 15% higher than costs for a CEA. Major stroke is a dominating factor in both quality of life and in follow-up costs. Therefore the short- and long-term results of the cost-benefit analysis will be highly influenced by the perioperative and post-operative incidence rates for major stroke. This idea is supported by model sensitivity analyses who show that the sensitivity to the long-term incidence rate is two times higher than the short-term incidence rate. As the level of uncertainty of the long-term major stroke rates are higher than those of the perioperative stroke rates, these will clearly dominate the level of uncertainty regarding the decision on the cost-effectiveness of the CAS procedure. CONCLUSIONS: The results show that the uncertainties concerning the long-term major stroke risks have a predominant influence on the outcome of the evaluation of the cost-effectiveness of CAS over CEA. Therefore, long-term effects need to be assessed and considered before a balanced decision on the cost-effectiveness of the CAS over the CEA procedure can be taken.