Alu elements are a prolific class of short interspersed elements (SINEs) that have expanded rapidly in the genomes of primates during the last 65 million years. Alu elements are non-autonomous and utilize the endonuclease/reverse transcriptase produced by long interspersed elements (LINEs) to copy and insert into new locations throughout the genome in a process known as retrotransposition. Alu insertions produce homoplasy-free genetic markers with known ancestral states. Subsets of lineage-specific and polymorphic Alu elements have been instrumental for resolving phylogenetic relationships among primates and for understanding genetic differentiation in humans. Alu elements contribute to genetic disease through insertional mutagenesis and non-allelic homologous recombination. Ongoing retrotransposition and Alu-mediated recombination are important evolutionary forces that continue to create new genetic diversity and reshape the genomes of humans and other primates.