[i] Lineage-specific Alu retrotransposition events were identified by analysis of human–chimpanzee orthologous genomic sequence. Extracted representative events (query sequences) were searched against a database of BAC end sequences (BES) which included 743,245 human BES (354,136,231 bp; Zhao et al. 2000) and 148,102 chimpanzee BES (115,468,024 bp; Fujiyama et al. 2002). Only full-length Alu elements were considered. When query sequence and BAC end-sequences were from the same species, a sequence similarity cutoff of 98.5% was used to account for sequencing errors within the single-pass BES database. When query sequence and BAC end sequences were from different species, sequence similarities greater or equal to 96.5% were counted (to account for sequencing error and species divergence). Human counts were further normalized by the size ratio of human and chimpanzee BAC end sequence library. *P < 0.05; **P < 0.01 by χ² test assuming equal distribution. In both cases, the human BES database shows a significant increase in the number of young Alu elements.