A consortium of researchers were involved in the sequencing project, which is aiming to explain why humans, but not chimps, succumb to diseases such as malaria, Alzheimer's disease and HIV.
Genetically, chimps and the related bonobo species are 98.6 per cent similar to humans, and working out where the differences lie could help explain why humans developed larger brains, upright spinal columns and more complex social behaviours.
The researchers expect to be able to point to which human genes and regions of the human genome are 'new', in evolutionary terms, and what genes in each species have been deleted through the many years of evolution.
Led by Eric Lander at the Broad Institute in Cambridge, Massachusetts, and Richard Wilson at Washington University School of Medicine in St Louis, Missouri, they started the programme in January of this year and have now arrived at four-fold coverage of the genome over 90 per cent of its length.
In addition, the draft has been made available in genome databases so that the job of comparing the sequence with the human version can begin.
A group in Japan is also working on the sequencing of the chimp genome, as well as other great apes, in an effort known as Project Silver. However, there has been some debate about whether it is sensible, given the finite sequencing resources available around the world, to focus on the chimp at all.
Other scientists have pushed to sequence the genomes of primates such as rhesus or macaque monkeys, as they are more commonly used in medical research. For similar reasons, efforts are already underway to sequence the rat, mouse and dog.