Introduction: An adequate sample of tissue is needed from EBUS to provide histopathology with sufficient material for molecular testing. Aims: To evaluate and compare a novel method of placing the first biopsy sample directly into the specimen pot (and then after, confirming identity using rapid on-site evaluation) rather than placing samples onto a slide first to confirm the identity, prior to placing them in to the specimen pot. Our hypothesis was that this would increase the availability of the samples for molecular testing. Method: The data from sixty samples processed prior to the change in practice was compared to sixty samples processed after. We also compared the prevalence of malignant tissue and the average number of needle passes made to obtain tissue; the latter to ensure any significant result was not due to another methodological variable. Results: Before the change in practice, 34 out of 60 (57%) cases were diagnosed as malignant. Twenty six of these were classed as non-small cell lung cancer. Out of the 24 cases sent for molecular testing, 16 were adequate for analysis (66.6%). The average number of passes per patient for those samples sent was 7. After placing the first sample in the specimen pot, 36 out of 60 cases (60%) were diagnosed as malignant. Thirty two of these were classed as non-small cell lung cancer. Out of the 32 cases sent for molecular testing, 24 were adequate for analysis (75%). The average number of passes per patient for these cohorts was 7 and 7.8, respectively. Conclusions: A “first sample into the pot” approach increases the sample yield available for molecular testing.