The reason for the comparison is the nature of the business Venter set up a year ago. His company intends, within three years, to map the human genome - to work out the sequence of chemicals along the whole length of human DNA, the molecule that is found in every living cell and contains the genetic code determining how our bodies develop.
It's a massive undertaking. There are three billion chemical building blocks that need to be placed in order, and the Human Genome Project, an international academic project with links to Cambridge, has been engaged in the task for 10 years.
Until a year ago, Venter was involved in the Human Genome Project, but he broke away to set up a private-sector rival, backed by $330m (pounds 206m) from Perkin-Elmer, an American maker of equipment used in genetic research. Venter is critical of the pace of the non-profit making Human Genome Project.
"It has been slow," he told the BBC's The Money Programme. "We have the best tools at the leading edge of technology. By the time you could develop that in most academic labs, the field would have moved on and there would be a new leading edge somewhere else."
The Human Genome Project, funded in Britain by the Wellcome Trust charity, is trying to avoid a public slanging match with Venter. But it has announced a huge increase in the pace of its work, so that the first draft of the human genome will be completed by next year. Both sides deny that this enormous task is becoming an undignified race.
The Bill Gates comparison is based on the assumption that being the first to produce a map of the human genome will give Venter's company, Celera Genomics, intellectual ownership of human genes, something potentially far more valuable than Bill Gates' ownership of the operating system of most of the world's personal computers.
It's a false comparison, according to Venter, because merely mapping the chemical bases along the length of human DNA will not give him any intellectual property rights. His business plan revolves around selling processed information about the human genome to big pharmaceutical companies. But Venter also plans to patent key genes that he identifies along the way, and that gives him the opportunity to make potentially lucrative licensing deals with major drug companies.
The issue of patenting human genes continues to divide the scientific community. The Human Genome Project is dedicated to putting all its findings into the public domain and its scientists are suspicious of gene patenting. "The trouble with patenting individual human genes is that it begins to restrict the flow of information," says David Bentley, one of the leaders of the Human Genome Project at the Sanger Centre, near Cambridge.
Although the existence of a patent does not prevent anyone from researching a gene, if they come up with a test or a treatment for a disease based on a patented gene, they have to do a deal with the patent-holder before their work can be commercialised. "It's a disincentive to others working on the same gene," says Dr Bentley. "So this reduces the amount of understanding that comes from the human gene sequence."
Venter's response is that patenting genes actually helps medical research. He argues that drug companies will not invest huge amounts of money in researching treatments based on genetic discoveries if they could find themselves pipped at the post by a competitor.
"Nobody is going to invest $600m to get a new drug on the market if they don't have intellectual property protection," he says.
Not surprisingly, much of the pharmaceutical industry agrees with him. They are happy to do deals with gene patent-holders if that stakes out a territory in which they can work exclusively. "My view on patenting genes is very simple," says George Poste, scientific director of SmithKline Beecham. "No patents, no cures."
Other sectors of the pharmaceutical industry plan to compete. Myriad Genetics and Incyte Pharmaceuticals in the US are already seeking profits from gene mapping.
So far the patenting of human genes has concentrated on the hunt for the genes associated with disease. But it will eventually encompass genes affecting other human characteristics: appearance, ageing, perhaps even intelligence. Observers like Jeremy Rifkin, author of The Biotech Century, warns that allowing intellectual ownership of these genes to fall into the hands of a small number of businesses could be disastrous.
According to Rifkin: "The idea that a handful of life science companies ought to be able to have a lock on the genetic blueprints of life on this planet for short-term commercial gains is simply scandalous. And I think if the public were asked in a survey: do you believe that these companies should be able to own the blueprints of life, virtually everyone would say 'no'."
Such opposition has done nothing to deter Venter. And while it may be far-fetched to think that he, or anyone else, will win a Microsoft-style monopoly in human genetics, there are other reasons for the Gates comparison.
Venter is not only a man with a scientific vision, he's a man in a hurry. In the year since he announced the formation of Celera he has taken on around four hundred employees, started to build the world's second-largest supercomputer (the US defence department is reckoned to have the biggest) and launched the company on the stock market.
He also has some of Bill Gates's personal intensity, in developing both his science and his business. His detractors say that Venter's problem is that he wants to be both a Nobel prize winner and a billionaire.
Venter denies any billionaire aspirations, but not all that strongly. "I think it's not bad to have aspirations in lots of directions," he says.
"We've set up a business model where Celera will only be successful if the science is absolutely leading edge, world-class science. That's the only way new medical breakthroughs will take place. You can't do that with mediocre science and mediocre laboratories."
n 'The Money Programme' will broadcast its special report on the business of human genetics, 'The Human Race', on BBC 2 at 7.30pm tonight.