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A high performance intelligent data acquisition system for QCM and other (superficial SAW and bulk acoustic wave) resonator-based chemical and biosensors described in this article. The system is based on the advanced frequency measurement technique using the modified method of the dependent count and allows obtaining high metrological performances: programmable and constant in all frequency range relative error of measurement up to 0.0005% that corresponds to 5 ppm; non-redundant, reduced conversion time of measurement and wide frequency range from 0.05 Hz to 9 MHz (144 MHz with prescaling). The developed system allows measuring variations of the resonance frequency shift and quartz crystal quality factor Q for QCM sensors working in liquids and gases. The described low-cost data acquisition system is based on novel integrated circuit of universal frequency-to-digital converter. This design approach has eliminated much of the hardware: there is no need for a microcontroller and complex sensor interfacing electronics, as it is directly compatible with PC computers.