HGP researchers deciphered the human genome using three tools: producing what are called linkage maps, complex versions of the type originated in early Drosophila research, through which inherited traits (such as those for genetic disease) can be tracked over generations; making maps that show the locations of genes for major sections of all our chromosomes; and determining the order, or "sequence," of all the bases in our genome's DNA.

The HGP already has revealed that there are probably somewhere around 30,000 human genes. The existing and ultimate products of the HGP will give the world a resource of detailed information about the structure, organization and function of the complete set of human genes and other functional elements found in DNA. This information can be thought of as the basic set of inheritable "instructions" for the development and function of a human being.

The International Human Genome Sequencing Consortium published the first draft of the human genome in the journal Nature in February 2001 with the sequence of the entire genome's three billion base pairs some 90 percent covered at an accuracy of 99.9%. A startling finding of this first draft is that the number of human genes appears to be significantly fewer than previous estimates, which ranged from 50,000 genes to as many as 140,000. The essentially complete 'finished' version of the human genome is scheduled to be completed two years earlier than originally anticipated, in April, 2003. Sequence finishing requires much more time and resources than the draft sequence, because all possible efforts are made to close gaps and resolve difficult regions. This final version will be 99.99% accurate at the base pair level and 95% of the three billion base pairs will be represented.

Upon publication of the draft of the genome, in February, 2001, Francis Collins, the director of NHGRI, noted that the genome could be thought of in terms of a book with multiple uses: "It's a history book - a narrative of the journey of our species through time. It's a shop manual, with an incredibly detailed blueprint for building every human cell. And it's a transformative textbook of medicine, with insights that will give health care providers immense new powers to treat, prevent and cure disease."