Background: Rapid on site examination (ROSE) is encouraged at endobronchial ultrasound transbronchial needles aspiration (EBUS-TBNA) to improve diagnostic yield. Due to new therapeutic options in lung cancer, it is not sufficient to merely distinguish between non-small cell lung carcinoma (NSCLC) and small cell lung carcinoma (SCLC). Immunohistochemistry (IHC) distinction is now standard practice, as well as additional molecular testing where clinically indicated. We investigated the diagnostic yield of on-site smears vs. cell block and the provision of cellular material for ancillary testing at our centre.Methods: A retrospective audit of all EBUS-TBNA procedures performed until July 2012 was undertaken.Diagnostic yield on smears versus cell block was recorded. Cell blocks were reviewed by an experienced pathologist to determine diagnostic accuracy and whether IHC and molecular testing were possible. Results: In total, 234 procedures were recorded with 101 (43.2%) malignant cases, 107 (45.7%) benign cases and an initial 26/234 (11.1%) insufficient for diagnosis of which 11/234 (4.7%) were false negatives for malignancy after further follow up. The average number of passes was 4.5. For malignancies, smear diagnosis was possible in 95% (96/101) of cases and cell block diagnosis in 93.5% (87/93) of cases. There was sufficient material for IHC in 97.7% (85/87) of malignant cases. In 79.3% (69/87) of NSCLCs molecular testing for epidermal growth factor receptor (EGFR) mutation analysis was theoretically possible on samples obtained. Conclusions: Cell blocks are not inferior to smears for diagnostic accuracy and provide sufficient samples for histology. However, ROSE assists the physician on how best to manage samples for ancillary testing.