In this paper, an IgE antigen concentration measurement system using a frequency-shift readout method for a two-port FPW (flexural plate-wave) allergy biosensor is presented. The proposed frequency-shift readout method adopts a peak detecting scheme to detect the resonant frequency. A linear frequency generator, a pair of peak detectors, two registers, and an subtractor are only needed in our system. According to the specification of the FPW allergy biosensor, the frequency sweep range is limited in 2 MHz to 10 MHz. The sensitivity of the peak detector is 0.8 mV. The proposed frequency-shift readout circuit is verified on silicon by using a standard 0.18 μm CMOS technology. The maximal power consumption is 12.94 mW@0.1 MHz clock given by HSPICE simulations.