Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin modifications are thought to play a key role in controlling TE activity. However, the mechanisms underlying this control are not well understood. Long-term experimental evolution of the nematode Caenorhabditis elegans has provided insights into the evolution of TEs. The results show that TEs are subject to purifying selection, which acts to remove deleterious mutations. This selection is thought to be mediated by the piRNA pathway. The study highlights the importance of TEs in shaping the evolution of eukaryotic genomes and provides new insights into the mechanisms underlying their control.