There is a need for robust techniques for early and accurate diagnosis of acute coronary syndromes (ACSs), to avoid inappropriate discharge of patients. This study examined the use of frequency spectrum analysis of heart rate variability (HRV) and photoplethysmogram (PPG) waveform variability for the identification of high-risk ACS patients defined by an elevated cardiac troponin level. The study cohort comprised a convenience sample of adult patients presenting to the emergency department of the Prince of Wales Hospital over a 4 month period complaining of non-traumatic chest pain. Valid electrocardiogram (ECG) and earlobe PPG waveforms together with troponin I test results were obtained from 52 patients at presentation, 4 of which were troponin I positive (Trop 0+). Frequency spectrum analysis was performed on the beat-to-beat HRV and PPG waveform variability (PPGV). The Trop 0+ were found to have significantly higher normalized mid-frequency power (MF(nu)) in HRV (P = 0.017), PPG amplitude variability (P = 0.009) and the cross-spectrum of HRV and PPGV (P = 0.001), which were attributed to reflex sympathetic response to myocardial ischemia. MF(nu) of PPG amplitude had the best overall performance in detecting Trop 0+, with ROC area under the curve of 0.93. The results demonstrate the potential use of ear PPG waveform to identify high-risk heart disease patients, and further highlight the utility of frequency spectrum analysis of PPGV in critical care.