Objective: To investigate the clinical implications and the impact of tissue artifacts on the histopathological diagnosis of oral lesions treated with a high-power 980 nm diode laser. Methods: This cross-sectional study utilized data from 2021 to 2023 from the Pathology Service of a university center. The research included histopathological records and surgical records of patients over 18 years old, diagnosed with oral lesions, and treated with a 980 nm diode laser. The selection of patients, who presented oral lesions with characteristics of benignity or potential malignancy, presented availability and completeness of clinical and demographic data and were submitted to oral biopsies using a Thera Lase Surgery® diode laser (DMC Equipamentos, São Carlos, Brazil). All procedures were performed by the same surgeon with the following parameters: 2.5–3.5 W output power, pulsatile mode (66.7 Hz pulse rate), 980 nm wavelength in the infrared emission range, the laser beam was delivered through a 400 μm optical fiber initiated, and the energy level of 100–130 J. All research activities were approved by the Human Research Ethics Committee of the institution where the research was conducted (68,828,923.5.0000.5417). Results: In the study, 12 patients aged 24 to 78 years underwent 13 oral biopsies using a 980 nm diode laser. The biopsied lesions were primarily located on the tongue and lip and displayed diverse clinical characteristics. During the procedures, there was no pain, bleeding, or need for sutures. Post-operative discomfort was reported in 23.07% of cases, with one reported infection. Although all samples exhibited tissue artifacts, such as margins carbonization and formation of intraepithelial blisters, the histopathological diagnosis was possible. Only in one case was an additional biopsy required due to thermal damage. Conclusion: This study highlights the promising potential of 980 nm diode laser use in oral surgeries, evidencing significant clinical benefits, and limitations. It emphasizes the need for awareness about tissue artifacts and the risks of incorrect diagnoses, stressing the necessity for more research to optimize the use of this laser and educating healthcare professionals about its implications. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2025.