Presence of transposable elements (TEs) in the human genome has profound effects on genome function, structure and evolution. TE mobility and inter-TE recombination are the origin of a large spectrum of mutations and genome reorganization leading to diseases. From the data provided by the Human Genome Project and from information on the detection and dynamics of TEs within and between species acquired during the last two decades, we now know that these elements are not only involved in mutagenesis but can also participate in many cellular functions including recombination, gene regulation, protein-coding RNA messages and, possibly, cellular stress response and centromere function. TEs also promote a general genome shuffling process that has been important for the evolution of several gene families and for the development of new regulatory pathways.