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Objective A multi-frequency complex impedance synchronous acquisition system for biological tissues is designed for the accurate determination of the composition of body fat, muscle and others in humans, which can overcome the fence effect.Methods According to the principle of frequency domain impedance measurement, a high-precision multi-frequency complex excitation source for impedance measurement is implemented based on field programmable gate array (FPGA) programming.And then a high signal to noise ratio adjustment and acquisition module suitable for weak signal is designed.Then an accurate discrete Fourier transform (DFT) analysis method is proposed to avoid the impact of the fence effect.Thus, an accurate and simple multi-frequency complex impedance synchronous measurement and analysis system is realized.Furthermore, human body RC model and contrast equipment are used to verify the accuracy of complex impedance and body composition measurement.Results The body impedance model measurement shows that the relative error of the system is not more than 1%, and themaximum error of phase angle is not more than 0.5 degrees.The correlation coefficients of body composition between our system and Tanita MC-180 are r=0.984 to 0.994 (P<0.001) .Conclusions The measurement results of the system are closely related to the results of MC-180.Meanwhile, the low complexity makes the equipment easy to be popularized, and provides an effective means for the large sample population census of body composition.