Purpose: We aimed to compare rapid eye movement sleep without atonia (RSWA), tonic RSWA, and phasic RSWA indices during polysomnography as a potential biomarker between narcolepsy type 1 and type 2. Methods: Medical files, polysomnography, and multiple sleep latency tests of patients with narcolepsy were evaluated retrospectively. A total of three adolescents and 31 adult patients were included. We calculated the total number of rapid eye movement (REM) epochs with tonic and phasic activity in accordance with the American Academy of Sleep Medicine manual scoring rules, version 2.4. We defined tonic RSWA index as the ratio of total number of REM sleep stage epochs with only tonic activity to total REM sleep stage epochs, phasic RSWA index as the ratio of total number of REM sleep stage epochs with only phasic activity to total REM sleep stage epochs, and RSWA index as the ratio of total number of REM stage sleep epochs with RSWA to total REM sleep stage epochs on the polysomnography. Results: Clinically and polysomnographically diagnosed 25 patients with narcolepsy type 1 and 9 patients with narcolepsy type 2 were included. The median age of the subjects was 30 (10, 61) and 36 (18, 64), respectively. Eleven narcolepsy type 1 patients (44%) and 4 narcolepsy type 2 patients (44.44%) were women. The RSWA index of >= 3% yielded a sensitivity of 76% and specificity of 88.9% (AUC = 0.77 (0.09), 95% confidence interval = 0.58 to 0.97, p = 0.01), and the tonic RSWA index of >= 2.2% yielded a sensitivity of 72% and specificity of 77.8% (area under the curve = 0.74 (0.1), 95% confidence interval = 0.54-0.94, p = 0.03). Conclusions: As an electrophysiological biomarker, RSWA and tonic RSWA indices can be sensitive and specific polysomnography parameters in distinguishing narcolepsy type 1 from narcolepsy type 2.