Claims about high genomic DNA sequence similarity between humans and chimpanzees are typically made to audiences that do not understand the various layers of technology and ideological bias imposed upon the origination of the data in question. The recent human-chimp Y-chromosome project introduced a number of important genomic tools to achieve a considerably less-biased analysis. The results indicated a much higher level of dissimilarity in both gene content and overall sequence similarity than the previously reported levels up to 99% similarity. As of yet, no similar study utilizing a less-biased genomic framework for autosomal regions has been reported. When evaluating comparisons between genomes using DNA sequence, it is important to understand the nature of how that sequence was obtained and bioinformatically manipulated before drawing any conclusions. It is not uncommon to arrange the sequence of a genome for which little is known by using the genome of a hypothetical closely related organism that has better developed genomic resources. It is also not uncommon to first screen the framework model genome to find regions of high similarity prior to any comparative analyses and to even omit gaps in the final DNA alignments before determining sequence identity. As a result, evolutionary bias literally colors every aspect of the DNA analysis and annotation. Understanding the technology used to produce a comparative genomic product for inter-genome studies is required prior to making any definitive conclusions about the data presented. At present, a considerably more unbiased approach to comparative genomics needs to be applied to the analysis and annotation of genome.