<b><i>Background:</i></b> During bronchoscopy, small biopsy forceps are increasingly used for the diagnosis of peripheral pulmonary lesions. However, it is unclear whether the formalin-fixed paraffin-embedded specimens sampled with the small biopsy forceps are suitable for the determination of genotypes which become indispensable for the management decision regarding patients with non-small cell lung cancer. <b><i>Objectives:</i></b> The aim of this study was to evaluate the feasibility and accuracy of molecular testing in the specimens obtained with 1.5-mm small biopsy forceps. <b><i>Methods:</i></b> We examined specimens in 91 patients, who were enrolled in our previous 3 studies on the usefulness of thin bronchoscopes and given a diagnosis of non-small cell lung cancer by bronchoscopy with the 1.5-mm biopsy forceps, and then underwent surgical resection. An experienced pathologist examined paraffin-embedded specimens obtained by bronchoscopic biopsy or surgical resection in a blind fashion on epidermal growth factor receptor <i>(EGFR)</i> mutations, anaplastic lymphoma kinase <i>(ALK)</i> rearrangements and <i>KRAS</i> mutations. <b><i>Results:</i></b> Twenty-five (27%), 2 (2%) and 5 (5%) patients had an <i>EGFR</i> mutation, <i>ALK</i> rearrangement and <i>KRAS</i> mutation, respectively, based on the results in surgical specimens. <i>EGFR, ALK </i>and <i>KRAS</i> testing with bronchoscopic specimens was feasible in 82 (90%), 86 (95%) and 83 (91%) patients, respectively. If molecular testing was feasible, the accuracy of <i>EGFR</i>, <i>ALK</i> and <i>KRAS</i> testing with bronchoscopic specimens for the results with surgical specimens was 98, 100 and 98%, respectively. <b><i>Conclusion:</i></b> The results of molecular testing in the formalin-fixed paraffin-embedded specimens obtained with the small forceps, in which the genotype could be evaluated, correlated well with those in surgically resected specimens.