The Genome Project proceeds towards the determination of the nucleotide sequence of the human genome. Meanwhile the total genomic sequences of some of the less complex organisms (E. coli, yeast, C. elegans and most recently Drosophila melanogaster) have already been determined. The identification and functional analysis of the genes constituting those genomes have remained one step behind. The simultaneous detection of the expression profiles of many mRNAs present in a given cell, tissue or organ have become possible by the recently developed DNA microarray technology. This approach will eventually lead to a higher level understanding of the molecular processes underlying the maintenance, regulation and mediation of all the functions of an organism governed by gene actions. However, the automated DNA chip technology by itself cannot replace the analysis of unique gene functions. New variants of the classical reverse genetic approach (i.e. from gene to function) based on random mutagenesis methods mu st be applied in a genome-wide scale to target every gene and conclude its role from the resultant phenotype. Two opposite mutagenesis methods, which complement each other well, exist one results in recessive loss-of function mutations by disrupting the targeted genes and the other generates dominant gain-of-function mutations by overexpressing or ectopically expressing the respective genes. The gene-trap methodology represents a powerful strategy by which functional genes can be easily cloned and identified. The method reliably generates the corresponding loss-of-function mutations simultaneously even if those are not manifested in any visible phenotype. These features make gene trapping particularly useful for genome analysis by allowing the correlation between the physical and genetic maps to be established.