Based on 56 rainfall stations, which cover the period 1961–2008, we analyzed the presence of trends in the drought-affected area over southern South America (SSA) at different time scales. In order to define drought conditions, we used the standardized precipitation index, which was calculated on time scales of 1, 3, 6, 9 and 12 months. The trends were estimated following both a linear and a non-linear approach. The non-linear approach was based on the residual of the empirical mode decomposition, a recently proposed methodology, which is robust in presence of non-stationary data. This assessment indicates the existence of reversals in the trends of the drought affected, area around the 1990s, from decreasing trends during the first period to increasing trends during the recent period. This is indicative of the existence of a low-frequency variability that modulates regional precipitation patterns at different temporal scales, and warns about possible future consequences in the social and economic sectors if trends towards an increase in the drought affected area continue.