The Institute of Applied Physics of the University of Berne is active in the filed of remote sensing of middle atmospheric trace gases such as ozone and water vapor by microwave radiometry. From the measured pressure broadened spectral lines it is possible to retrieve the vertical distribution of the observed species. One of the radiometers is operating from an aircraft of the Swiss Air Force. For the spectral analysis it uses a broadband acousto-optical spectrometer with a total bandwidth of 1 GHz with 1725 channels, which allows retrievals of altitude profiles from about the flight height up to 60 km. Unfortunately acousto-optical spectrometers proved to be critical under conditions encountered in an aircraft. For this reason the novel approach of using digital Fast Fourier Transform (FFT) spectrometers with a total bandwidth of 25 MHz and with the option to select either 2048 or 4096 channels and another FFT spectrometer with 16384 channels on 1 GHz bandwidth was chosen. In this paper we present first measurements of atmospheric trace constituents using this novel approach with digital FFT spectrometers. We report on critical instrumental aspects such as system stability and linearity that are of fundamental importance for this application.