Eukaryotic genomes contain millions of copies of repetitive elements (RE). Although the euchromatic parts of most genomes are clearly annotated, the repetitive/heterochromatic parts are poorly defined. It is estimated that between 50 and 70% of the human genome is composed of REs. Despite this, we know surprisingly little about the physiological relevance, molecular regulation and the composition of these regions. This primarily reflects the difficulty that REs pose for PCR-based assays, and their poor map-ability in next generation sequencing experiments. Here we first summarize the nature and classification of REs and then examine how this has been used in the recent years to broaden our understanding of mechanisms that keep the repetitive regions of our genomes silent and stable.