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Accurate amplitude and phase difference estimation is desired for impedance measurements where two common frequency sine signals are acquired. One of the proposed algorithms for amplitude and phase estimation is the ellipse fitting algorithm. This algorithm, due to its simplicity, is a prime candidate for implementation in standalone impedance measurement systems based on DSPs. However, the phase difference estimation of the ellipse fit method is biased when the signals approach in phase or in phase-opposition. In this paper, a modified ellipse fit method is proposed to improve phase difference estimation. The performance of the algorithm is tested on simulated data. It is found that the proposed method is better for phase difference estimation than the ellipse fit method.