OBJECTIVES: The prevalence of thyroid nodules is high with four to seven percent in the general population. Fine-needle aspiration cytology (FNA-t) is recommended as the reference test because it is minimally invasive, presents an optimal positive predictive value and is cost-effective when compared to whole-body-scan (WBS). The diagnosis is known for the fraction of patients operated. Suspicious findings are a dilemma. For benign and indeterminate results, a long-term follow-up delayed the time of diagnosis. This study aims to determine the total cost of a true diagnosis by FNA-t. The model takes account of false-positive, false-negative, suspicious and indeterminate results. METHODS: A Markov model was built describing the trajectory and the management of patients, from the first FNA-t and until a conclusive diagnosis was obtained. We derived estimates for patient, diagnostic accuracy values and follow-up from a retrospective study, including patients who had their first FNA-t in 2003 or 2004. Costs were computed from the viewpoint of the hospital. A microcosting study was assessed to determine the unit cost of FNA-t. Costs of hospital stays for surgery were extracted from the hospital cost accounting. Sensitivity analyses were performed. RESULTS: A total of 105/390 patients were operated. Specificity and sensitivity values were respectively 86% and 78%. The unit cost of FNA-t was estimated to €118. Markov modeling showed that the mean total cost of a true diagnosis was €997 per patient, including unnecessary surgeries, FNA-t and follow-up. Cost decreased with the capacity of the cytologist to minimize indeterminate results. CONCLUSION: The true cost of a given procedure exceeds its unit cost of production. This result is conditional to the performance of the cytologist and is highly dependent on the 29% of indeterminate results. Ultrasound-guidance would reduce this rate and the true cost by a great deal at a relatively low unit cost.