The human genome is pervasively transcribed and produces a wide array of long noncoding RNAs that have been implicated in gene regulation, chromatin modification, nuclear organization, and scaffolding for functionally active protein complexes. Of particular interest in human origins is the long and very long intergenic noncoding RNAs transcribed from genomic regions outside protein coding genes. These are known as lincRNA and vlincRNA, respectively. LincRNA regions of the genome are more taxonomically restricted than protein coding segments and make logical candidates for research in genomic discontinuity. This report describes the comparative use of three different human lincRNA datasets and one vlincRNA dataset to the chimpanzee genome using the BLASTN algorithm. Short human lincRNA genomic regions (less than 600 bases) were about 75–79% similar to chimpanzee, while the larger lincRNA regions (greater than 600 bases) were about 71 to 74% similar. The human vlincRNA genomic regions were only 67% similar to chimpanzee. In contrast, all known human protein coding exons 300 to 599 bases in length, are 86% similar to chimpanzee.