Atmospheric and oceanic variability in the Arctic shows the existence of several oscillatory modes. The decadal-scale mode associated with the Arctic Oscillation (AO) and a low-frequency oscillation (LFO) with an approximate time scale of 60–80 years, dominate. Both modes were positive in the 1990s, signifying a prolonged phase of anomalously low atmospheric sea level pressure and above normal surface air temperature in the central Arctic. Consistent with an enhanced cyclonic component, the arctic anticyclone was weakened and vorticity of winds became positive. The rapid reduction of arctic ice thickness in the 1990s may be one manifestation of the intense atmosphere and ice cyclonic circulation regime due to the synchronous actions of the AO and LFO. Our results suggest that the decadal AO and multidecadal LFO drive large amplitude natural variability in the Arctic making detection of possible long-term trends induced by greenhouse gas warming most difficult.