Transposable elements have been shaping the genome throughout evolution, contributing to the creation of new genes and sophisticated regulatory network systems. Today, most of genomes (animals and plants) allow the expression and accommodate transposition of a few transposon families. The potential genetic impact of this small fraction of mobile elements should not be underestimated. Although new insertions that happen in germ cells are likely to be passed to the next generation, mobilization in pluripotent embryonic stem cells or in somatic cells may contribute to the differences observed in genetic makeup and epigenetic gene regulation during development at the cellular level. The fact that these elements are still active, generating innovative ways to alter gene expression and genomic structure, suggests that the cellular genome is not static or deterministic but rather dynamic. In this short review, we collect a set of recent observations that point to a new appreciation of transposable elements as a source of genetic variation.