The validity of using chimpanzees to investigate human diseases is frequently asserted via claims of the 98-99% genetic similarity between humans and chimpanzees. Critical analyses of the relevance of chimpanzee studies to human biology, however, indicate that this genetic similarity does not result in sufficient physiological similarity for the chimpanzee to constitute a good model for research, and that there is a lack of translation of chimpanzee data to clinical practice and progress. Examples include: the minimal citation of chimpanzee research relevant to human medicine; highly different pathology of HIV/AIDS and hepatitis C virus infection and lack of correlation of vaccine and treatment efficacy for these diseases; lack of usefulness in cancer research; and others. The major molecular differences underlying these interspecies phenotypic disparities have been revealed by comparative genomics and molecular biology: namely, key differences in all aspects of gene expression, from chromosome structure through to post-translational modifications. The collective effects of these differences are striking, extensive and widespread, and show the superficial similarity between human and chimpanzee genetic sequences to be of little consequence for biomedical research. The extrapolation of biomedical data from the chimpanzee to the human is therefore highly unreliable, and the chimpanzee model must be considered of little value, particularly given the breadth and potential of alternative methods of scientific enquiry currently available to science.