The aim of this study was to characterize left atrial appendage mechanical function in atrial fibrillation and flutter by Fourier analysis to analyze frequency and regularity of flow. Left atrial appendage function is central to a patient's risk for thromboembolism. Although the function of the appendage can be analyzed by Doppler echocardiography in sinus rhythm, its mechanical function in atrial fibrillation and flutter has not been well characterized. This lack of adequate definition is caused by the complexity and temporal variability of the Doppler flow profiles. We assessed left atrial appendage function in 21 cases of atrial fibrillation (n - 11) and flutter (n = 10) and five in sinus rhythm with transesophageal Doppler echocardiography. Doppler profiles were examined by Fourier analysis, and the power spectra compared and analyzed between patients with atrial fibrillation and flutter. Left atrial appendage Doppler flow in atrial fibrillation produced Fourier spectra over a narrow band of frequencies with a peak frequency of 6.2 +/- 1.0 Hz, significantly higher than in atrial flutter (3.9 +/- 0.6 Hz, p < 0.00001). Additionally, a significant difference in subharmonic modulation (spectral power below the peak frequency) was observed between atrial appendage flow in atrial fibrillation and flutter, because 37% +/- 16% of the total spectral power was achieved before the dominant frequency in atrial fibrillation compared with 20% +/- 14% in atrial flutter (p = 0.02). Conversely, patients in sinus rhythm exhibited broad-banded Fourier spectra with most of the power in discrete frequency spikes at harmonics above the fundamental frequency with very little subharmonic modulation (1% +/- 0.05%). Left atrial appendage function in atrial fibrillation and flutter can be well characterized by Fourier analysis of Doppler flow. Atrial fibrillation has higher dominant frequencies and greater subharmonic modulation compared with flutter. Moreover, atrial fibrillation demonstrated quasiperiodic contraction patterns typically found in chaotic systems. Fourier analysis of left atrial appendage contraction patterns may therefore have significant promise in providing insights into mechanisms of atrial fibrillation and thromboembolism.