They say their findings could explain why people get Alzheimer's disease, certain cancers and even AIDS, which chimpanzees do not.
The researchers also say their findings are further proof that evolution is real and works through natural selection, just as Charles Darwin predicted a century ago.
Dr. Francis Collins, head of the National Human Genome Research Institute, which funded the studies, says as our closest relatives, the chimpanzees tell us special things about what it means to be a primate and, ultimately, what it means to be a human at the DNA level.
In the research Dr. Robert Waterston of the University of Washington in Seattle and colleagues sequenced the DNA of a chimpanzee named Clint, who is now dead.
They then compared it to the human genome sequence and did a letter-by-letter comparison of the DNA base pairs, the A, C, T and G nucleotides that make up both the human and chimp genetic codes.
They found that out of 3 billion base pairs, that make up both the human and the chimpanzee genomes, only 40 million differ between human and chimp.
It seems that most are changes in a single letter, for instance a human has an A where a chimp has a T, humans have some extra DNA that chimps do not have and vice-versa.
As all these differences add up to just 4 percent of the total genomes, it means humans and chimps are 96 percent identical, genetically.
Waterston says if a difference is seen between a chimp and a human, it is clearly the result of a single evolutionary event, and within those 40 million events, we clearly have the basis for what makes us human.
Dr. LaDeana Hillier of Washington University says that humans and chimps evolved separately from a common ancestor that lived about 6 million years ago and three different types of genes seem to have evolved rapidly in both humans and chimpanzees, those involved in reproduction, smelling and immunity.
Tarjei Mikkelsen, a graduate student at the Broad Institute, a joint venture of the Massachusetts Institute of Technology and Harvard University who led one study, says that the vast majority of these 40 million changes are probably not relevant to what makes us human because they are in junk DNA, and only about 5 percent affect proteins that are likely to have a large effect on biology.
Among them is a parasite related to sleeping sickness that infects chimps but not humans, and one gene for sialic acid, which is found on the surfaces of cells and is used by some viruses to infect them.
Mikkelsen says there is also an enzyme called caspase 12, which is mutated in humans and appears to make our species susceptible to the brain-wasting Alzheimer's disease.
The researchers said their findings clearly contradicted an increasingly vocal movement in the United States that disputed the science of evolution and instead called for teaching creationism or the idea of intelligent design to school children.
Waterston says their work is a look at evolution in action, and a strong confirmation of Darwin's ideas when the human and the chimpanzee genome are compared.
Collins does add that the study did not address philosophical or religious questions, and may not explain other aspects of humanity, such as how do humans tell right from wrong.
The study is published in the journal Nature.