We compared the diagnostic performances of conventional smears and cell block preparations of tissue samples obtained with endobronchial ultrasound-guided transbronchial needle aspiration. We retrospectively analysed 451 patients (926 lymph nodes) who had undergone endobronchial ultrasound and for whom both smears and cell blocks were available and compared the diagnostic performances of these techniques when used alone and combined. Cell block preparations showed higher diagnostic performance over smears, but the combination was superior to either alone. The combination of smear and cell block techniques achieved a sensitivity, specificity and positive and negative predictive values of 92.5, 100, 100, 97.7 and 99.4, 95.0, 98.6, and 97.9 % for malignant and benign diseases, respectively. We recommend cell block preparations during endobronchial ultrasound-guided transbronchial needle aspiration.