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The purpose of the study is to evaluate Auditory Evoked Potentials (AEPs) in patients with hyperthyroidism and to compare their frequency components with those of healthy subjects. In this study the AEPs in hyperthyroidism were studied both in time and frequency domains rather than studying just in the time domain by peak scoring. This paper presents a method for filtering auditory oddball standard and target AEPs by using singular spectrum analysis (SSA) and feature extraction in the frequency domain via spectral analysis. AEPs were recorded during an auditory oddball paradigm in 25 newly diagnosed hyperthyroid patients and 15 healthy subjects. The signals are captured in the presence of ongoing background EEG activity so they are often contaminated by artifacts. This paper presents a method for filtering auditory odd-ball standard and target AEPs by using Singular spectrum analysis and feature extraction in frequency domain via spectral analysis. Information about the frequency composition of the signal is then used to compare normal and hyperthyroid states. While there was no significant difference either in the target or standard unfiltered signals between the hyperthyroid patients and the control group (p > 0.05), there was a significant difference in the filtered signals between the two groups (p < 0.01). In conclusion, our results revealed that SSA is an effective filtering method for AEPs. Thus, a much more objective and specific examination method was developed.