Antisense transcripts can influence the sense partner gene function by modifying the transcriptional and/or posttranscriptional regulation processes. Here, we report the identification of 13 cases of human-specific antisense transcripts induced by transposable element insertions from the analysis of primate genome alignment and human transcriptome data. The original sources of the insert included L1, Alu, SVA and human endogenous retrovirus (HERV). In the majority of the cases, insertion of a transposable element served as a promoter and drove transcription of the adjacent genomic segment, creating a novel antisense transcriptional unit (for examples, RNF144A, SYNE2, CAMCK4 and LSAMP). In the remaining cases, an existing antisense transcript was modified upon insertion; the insert supplied a promoter (ABCA9), an internal exon (LHFPL3 and DSG1) or a terminal exon (TEX11). We propose that creation of human-specific antisense transcripts may have altered the partner gene function and consequently may have played a role in the acquisition of various human-specific traits.