Genetic transformation of cereal crops is a powerful research tool for analysis of gene function and varietal improvement. Application of the method is possible when the expression of introduced transgene is on the desired level and stable over several generations. The production of transgenic cereals was mainly performed by microprojectile bombardment. However, some advance was also achieved by application of Agrobacterium-mediated transformation. For rice, which is the cereal model species, this method is routinely used, while for many others, especially polyploids, it has been developed very recently and only in a few laboratories. We still lack the knowledge whether the main features of Agro-mediated transformation (i.e. integration of one or few copies usually not rearranged and well defined transgene cassette) influence the transgene expression in polyploid cereal species. This review discusses known mechanisms possibly involved in transgene silencing, using both transformation methods. Part of the discussion is focused on transgene expression / silencing in relation to large genomes of polyploid cereals. Another application of genetic transformation, based on RNAi technology (RNA interference), is silencing of selected genes. This could be used to study gene function as well as to induce silencing of the native, single or family genes of cereals. Two strategies of silencing are discussed: a strategy of transcriptional gene silencing (TGS) and posttranscriptional gene silencing (PTGS).