The objective of this study was to assess the utility of endobronchial ultrasound (EBUS) morphology of lymph nodes in predicting benign cytology of transbronchial needle aspirates in a prospective observational study. Five ultrasonic morphological characteristics of mediastinal and hilar lymph nodes were recorded: size, shape, margins, echogenic appearance and the presence of a central blood vessel. These characteristics were correlated with the final diagnosis. A total of 402 consecutive patients (237 males and 165 females) undergoing EBUS were studied. The final diagnosis was malignant disease in 244 (60.6%) and benign disease in 153 (38.05%) subjects. Out of 740 sampled nodes, in 463 (62.6%) malignant cells were identified, whereas in 270 (36.5%) nodes, no malignant cells were identified. On univariate analysis small size, triangular shape and the presence of a central vessel were predictive of a benign aetiology. In the final multivariate model, a predictive probability of 0.811 (95% CI 0.72–0.91) for benign disease was found if lymph node size was <10 mm and a central vessel was present. Sonographic appearances of lymph nodes improve the predictive probability of EBUS for benign aetiologies, and may reduce the number of nodes requiring sampling and the need for further invasive investigations.