Atmospheric instability indices are routinely used in operational forecasting for identifying the possibility of convective storm activity. This study focuses on the long-term temporal assessment of Showalter Index, SWEAT Index, K- Index and CAPE at three coastal (Athens, Istanbul and Brindisi) and at one inland station (Sofia) of southeastern Europe. The indices are calculated from daily archived radiosonde observations for a 36-year period, from 1973 to 2008. In order to identify meaningful temporal trends, a two-phase methodology is applied. The first step contains the assessment of the monthly, seasonal and yearly averages. The yearly trends of Showalter and SWEAT indices indicate an increase of atmospheric instability mean values for Athens, Brindisi and Sofia after mid 1990s. The second step, which is the primary focus of this study, is the assessment of index extremes. After the selection of index threshold levels, index extremes are studied in terms of threshold exceedences. The analysis reveals long term trends for some combinations of indices and stations.