We have analyzed intergenic distances and searched for the presence of bidirectional genes using the complete sequences and mapping information of human chromosomes 20, 21, and 22, which contain 2,122 known and predicted genes. Intergenic distances between genes with divergent transcripts were distributed in a biphasic manner with a strong peak of 25 kb and a weak peak of 0.3 kb between the divergent transcripts, suggesting that the genes might share a common promoter. The weak peak was not observed at the transcriptional ends of genes. Seventy-three percent (55/75 pairs of genes, from a total of 150 genes) of these divergent transcripts located within 1 kb of one another were CpG islands. Expression of the divergent transcript genes was not concordant in various human tissues, suggesting that they were independently regulated. Analyses of the frequency of occurrence of interspersed repeats in the intergenic sequences suggested that these repeats are strongly excluded from the regions of transcriptional starts. This exclusion might be responsible for the existence of these divergent transcripts.