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Endobronchial ultrasound (EBUS) and electromagnetic navigation bronchoscopy (ENB) have increased the diagnostic yield of bronchoscopic diagnosis of peripheral lung lesions. However, the role of combining these modalities to overcome each individual technique's limitations and, consequently, to further increase the diagnostic yield remains untested.A prospective randomized controlled trial involving three diagnostic arms: EBUS only, ENB only, and a combined procedure.All procedures were performed via flexible bronchoscopy and transbronchial forceps biopsies were obtained without fluoroscopic guidance. In the combined group, after electromagnetic navigation, the ultrasound probe was passed through an extended working channel to visualize the lesion. Biopsies were taken if ultrasound visualization showed that the extended working channel was within the target. Primary outcome was diagnostic yield. The reference “gold standard” was a surgical biopsy if bronchoscopic biopsy did not reveal a definite histological diagnosis compatible with the clinical presentation. Secondary outcomes were yields by size, lobar distribution, and lesion pathology. Complication rates were also documented.Of the 120 patients recruited, 118 had a definitive histological diagnosis and were included in the final analysis. The diagnostic yield of the combined procedure (88%) was greater than EBUS (69%) or ENB alone (59%; p = 0.02). The combined procedure's yield was independent of lesion size or lobar distribution. The pneumothorax rates ranged from 5 to 8%, with no significant differences between the groups.Combined EBUS and ENB improves the diagnostic yield of flexible bronchoscopy in peripheral lung lesions without compromising safety.