We provide the first ever characterization of the primary modes of ionospheric Hall and Pedersen conductance variability as empirical orthogonal functions (EOFs). These are derived from six satellite years of Defense Meteorological Satellite Program (DMSP) particle data acquired during the rise of solar cycles 22 and 24. The 60 million DMSP spectra were each processed through the Global Airlglow Model. Ours is the first large-scale analysis of ionospheric conductances completely free of assumption of the incident electron energy spectra. We show that the mean patterns and first four EOFs capture ~50.1 and 52.9% of the total Pedersen and Hall conductance variabilities, respectively. The mean patterns and first EOFs are consistent with typical diffuse auroral oval structures and quiet time strengthening/weakening of the mean pattern. The second and third EOFs show major disturbance features of magnetosphere-ionosphere (MI) interactions: geomagnetically induced auroral zone expansion in EOF2 and the auroral substorm current wedge in EOF3. The fourth EOFs suggest diminished conductance associated with ionospheric substorm recovery mode. We identify the most important modes of ionospheric conductance variability. Our results will allow improved modeling of the background error covariance needed for ionospheric assimilative procedures and improved understanding of MI coupling processes.