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Isolated REM sleep behaviour disorder (iRBD) represents a prodromal stage of alpha-synucleinopathies, frequently preceding Parkinson’s disease and dementia with Lewy bodies. Beyond the characteristic sleep disturbances, alterations in brain-body coupling, reflecting neural peripheral physiological interactions, have yet to be determined. Using whole-night polysomnography, we quantified brain-body coupling via heartbeat evoked potentials (HEPs) across wakefulness, NREM, and REM sleep. Individuals with iRBD ( n = 13) were compared with healthy controls ( n = 23), alongside analyses of ECG-derived features. During wakefulness, iRBD patients showed altered HEPs over frontal regions between 305 and 445 ms after the R-peak. No significant group differences were observed during NREM or REM sleep, and HEP amplitude alterations were not explained by ECG differences. These diurnal HEP changes may represent a novel quantitative biomarker for iRBD during wakefulness and, in the future, could serve as a marker for phenoconversion to alpha-synucleinopathy.