Background Assessment of mediastinal lymph nodes is recommended in patients with non-small cell lung cancer without distant metastases. Linear transoesophageal endoscopic ultrasound with real-time guided fine-needle aspiration (EUS-FNA) is a promising non-surgical tool for mediastinal staging. We conducted a randomized controlled trial comparing surgical staging with EUS-FNA. Patients and methods Patients with proven or suspected non-small cell lung cancer in whom mediastinal exploration was required, were randomly assigned to undergo EUS-FNA or the appropriate surgical staging procedure. When EUS-FNA did not show malignant lymph node invasion, a confirmatory surgical staging procedure was done. A negative surgical staging procedure was followed by thoracotomy with systematic lymph node sampling. The primary endpoint was the rate of surgical staging interventions. The secondary endpoints were test performance of EUS-FNA and surgical staging, morbidity and length of hospital stay, considering surgical staging was performed as an in-patient procedure. Results Forty patients were randomized: 19 to EUS-FNA and 21 to surgical mediastinal staging. Patient and tumour characteristics were well balanced between both groups. For patients allocated to EUS-FNA, surgical staging was needed in 32% (P<0.001). The sensitivity to detect malignant lymph node invasion was 93% (95% CI 66-99) for EUS-FNA and 73% (95% CI 39-93) for surgical staging (P=0.29). Complication rate was 0% for EUS-FNA and 5% for surgical staging (P=1.0). The median hospital stay was significantly shorter for EUS-FNA versus surgical staging (0 vs 2 nights, P<0.001). Conclusion EUS-FNA reduces the need for surgical staging procedures in patients with (suspected) lung cancer in whom a mediastinal exploration is needed. www.clinicaltrials.gov (NCT00119470)