The capacity of human transposable elements (TEs) to promote cis natural antisense transcripts (cis-NATs) is revealed by the discovery of 48,718 human gene antisense transcriptional start sites (TSSs) within TE sequences. TSSs that yield cis-NATs are overrepresented among TE sequences, and TE-initiated cis-NATs are more abundant close to the 3' ends of genes. The TE sequences that promote antisense transcription within human genes are relatively ancient, suggesting that selection has acted to conserve their function.