But researchers at the Georgia Institute of Technology now say they've determined that it's the insertion and deletion of large pieces of DNA near genes that causes the differences.
While the DNA sequence of genes between humans and chimpanzees is nearly identical, there are large genomic 'gaps' in areas next to genes that can affect the extent to which the genes are 'turned on' and 'turned off'.
And the new research shows that these genomic gaps are mainly due to the insertion or deletion of viral-like sequences called retrotransposons that are known to comprise about half of the genomes of both species.
"These genetic gaps have primarily been caused by the activity of retroviral-like transposable element sequences," says biology professor John McDonald.
"Transposable elements were once considered 'junk DNA' with little or no function. Now it appears that they may be one of the major reasons why we are so different from chimpanzees."
His team examined the genomic gaps in both species, and found they were significantly correlated with already-established differences in gene expression.
"Our findings are generally consistent with the notion that the morphological and behavioral differences between humans and chimpanzees are predominately due to differences in the regulation of genes rather than to differences in the sequence of the genes themselves," says McDonald.