Abstract A capacitive biosensor based on vertically paired electrodes with controlled parasitic capacitance is presented to improve the sensitivity of capacitive measurement. The vertically paired electrodes were fabricated with a parylene film as a dielectric layer, with the distance between the electrodes less than hundreds of nanometer. The problem of parasitic capacitance owing to the electrode configuration was analyzed according to the superposed area of the electrode. In this work, two kinds of vertically paired electrodes were fabricated to control the parasitic capacitance—square-type and circular-type electrodes with different superimposed areas of 21.8 (100%) and 9.3 (42%) mm2 and the same electrode area of 9.4 × 10−5 mm2, respectively. The effect of superimposed area of the vertically paired electrodes on capacitive measurement was analyzed using the electrodes. The sensitivity of capacitive measurement was observed to increase with a decrease in superimposed electrode area and frequency. Further, the effect of parasitic capacitance was estimated by computer simulation of the sensitivity of impedance and capacitive measurement when 10% change in RS or CS occurred. The results showed that adsorption of proteins could be sensitively measured when the parasitic capacitance decreased. Finally, the effect of superimposed area of the vertically paired electrodes was measured from the interaction between antigens (human serum albumin, HSA) and immobilized antibodies (anti-HSA antibodies).