Transposable elements (TE), defined as discrete pieces of DNA that can move from one site to another site in genomes, represent significant components of eukaryotic genomes, including primates. Comparative genome-wide analyses have revealed the considerable structural and functional impact of TE families on primate genomes. Insights into these questions have come in part from the development of computational methods that allow detailed and reliable identification, annotation, and evolutionary analyses of the many TE families that populate primate genomes. Here, we present an overview of these computational methods and describe efficient data mining strategies for providing a comprehensive picture of TE biology in newly available genome sequences.