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Proteases and their specific inhibitors are ubiquitously distributed and play a key regulatory role in many biological processes. Gene expression and activity of certain proteases has been shown to increase in Triticum aestivum L. leaves under drought, with a major contribution of cysteine proteases, especially in sensitive wheat varieties. However, little is known about the stress response of protease inhibitors (PIs) and their role in the regulation of intracellular proteolysis. In this study the changes in transcript abundance of some protease inhibitors (belonging to cystatin and serpin classes) were evaluated by semi-quantitative RT-PCR in leaves and roots of winter wheat seedlings from two varieties with differing tolerance. The expression of two cysteine proteases in the same samples was also assessed. The expression of the studied genes was compared in the tolerant variety "Katya" and the more susceptible to water deprivation variety "Sadovo", applying severe but recoverable soil drought. Growth inhibition and stress related parameters confirmed the relatively higher drought sensitivity of variety "Sadovo". Serpin transcript abundance in control roots was higher than in the leaves. An opposite trend was documented for cystatins - the level of their expression was stronger in the non-treated leaves compared to roots. Drought stress inhibited PI expression in roots, while varying effects on the transcript levels were detected in the leaves of water deprived plants. The levels of the two cysteine protease transcripts under drought exhibited organ-specific response - they declined in roots, and increased in leaves. Further detailed studies using more sensitive methods are necessary to evaluate the potential of protease inhibitors as biochemical markers for drought tolerance. [ABSTRACT FROM AUTHOR]