The aim of this study was to assess the efficacy of the Identafi system in the screening of oral malignant and potentially malignant lesions over a conventional oral examination (COE). The study was a diagnostic clinical trial, in which 599 tobacco users were assessed through COE. The examination was repeated using the Identafi system. Biopsies of suspicious lesions served as the gold standard for evaluation of the validity of the technique. The Identafi showed 93.4% sensitivity and 98.9% specificity versus COE. When histopathology served as the gold standard, both techniques had a sensitivity and a specificity of 80.0 and 14.7%, respectively. Furthermore, the Identafi system achieved 100% sensitivity versus 0% sensitivity when it was used by a consultant versus a general dentist; however, poor specificity was observed for both techniques when performed by any practitioner. According to clinician feedback, the Identafi enhanced lesion visibility and led to the identification of a few additional new lesions. However, this system did not alter the diagnosis or biopsy sites. The Identafi system is a simple, noninvasive test that can facilitate the identification of potentially malignant oral lesions when applied by an experienced clinician.