It has been over ten years now since genetically modified plants, obtained due to genetic transformation, started to be cultivated in many countries all over the world. As a rule, a GM plant is characterized by a new trait developed as a result of gene/genes (T-DNA), derived from another organism. It seems that no in sufficient attention has been paid to the fact that genetic transformation has provided a useful tool for functional plant genomics. The identification of genome sequences of a few species (such as Arabidopsis thaliana, Oryza sativa i Medicago truncatula) and significant progress in genome sequencing of some others, including trees (Populus trichocarpa), lead to an inevitable question about the function of genes. It is the knowledge of the function of DNA sequences that allows for their practical applications. Insertional mutagenesis, based on T-DNA incorporation, meant to cause gene modification resulting in the development of new plant phenotypes. Mutant phenotype ensures isolation and identification of the modified gene. In order to identify the function of a gene which does not bring about phenotype changes, it is necessary to supplement an inserted DNA segment with sequences enabling the monitoring of gene expression. Gene silencing technology is another way to get the information about gene function and to control genes. New techniques are being enriched with improved chemical and physical mutation methods. Further studies and new applications are greatly facilitated by the detection of gene functions with the use of insertional mutagenesis, gene silencing strategy and evaluation of gene expression.