The emergence of Electromagnetic Navigational Bronchoscopy (ENB) as a diagnostic tool for small peripheral lung nodules has introduced a new method for delivery of fiducial markers. This technique has not been well studied in the literature. The purpose of our study was to evaluate the safety and effectiveness of ENB when used in fiducial marker placement. We reviewed all patients undergoing ENB fiducial placement between June 2010 and February 2014 (n = 64). These 64 patients had 68 lung lesions, in which we placed a total of 190 markers. Primary end points were marker retention and postoperative complications. The retention rate for the study was 82 per cent (n = 156). Upper lobe lesions had a 78 per cent retention rate and the middle/lower lobe lesions had an 89 per cent retention rate; the difference was not significant (P = 0.126). Complications included hospital admissions, respiratory failure, and pneumothorax. The difference in complication rates between upper and middle/lower lobe markers was not significant. We found ENB to be a safe method for the placement of fiducial markers. We also found that placement of an average of three markers/lesion led to an adequate retention rate to allow for successful treatment of lung cancer in nonsurgical patients using lung-sparing stereotactic radiation.