The author of God is Not Great: How Religion Poisons Everything said that he is a "guinea pig" for a new personalised medicine partly developed by Dr Francis Collins, a geneticist with very strong religious views.
The two had often met in the past as adversaries in the debate about whether God exists.
Against the odds they had become friends.
Now Hitchens is one of the few people in the world who has had his entire genetic make up mapped and is receiving a new treatment that targets his own damaged DNA.
"I’m an experiment," Hitchens said.
"These are early stages, but in theory it should attack the primary site of the tumour.
"If that does happen, it won’t just be good news for me, it will be very exciting in the general treatment of cancer."
Dr Collins is a former director of the National Human Genome Research Project and is now the director of America’s National Institutes of Health.
He is the author of a bestselling book, The Language of God: A Scientist Presents Evidence for Belief.
"It is a rather wonderful relationship,’ said Hitchens.
"I won’t say he doesn’t pray for me, because I think he probably does; but he doesn’t discuss it with me.
"He agrees that his medical experience does not include anything that could be described as a miracle cure – he’s never come across anything."
Hitchens, 61, originally from Portsmouth but now living in Washington DC, is an old Oxford University friend of the writer Martin Amis and has had a long journalistic career on both sides of the Atlantic.
In September 2005, he was named one of the "Top 100 Public Intellectuals" in the world by Foreign Policy and Prospect magazines.
Since the publication of his book he has become a hero of so-called New Atheism movement.
His pre-eminence has been enhanced by his steadfast refusal to change his views even after he was diagnosed with cancer of the oesophagus last year.
The prognosis looked very grave until a few weeks after his diagnosis he was asked if he would like to be a guinea pig in the new science of genome sequencing as a possible cure for cancer.
Samples were taken from healthy tissue and from his tumour and on each of them six billion DNA matches were run, in order to catalogue any mutations found in the cancerous cells.
He was warned to have no expectations.
But in the New Year came the good news that there is a genetic mutation found in the tumour for which there already exists a drug.
Having been on varying types and doses of chemotherapy, he is now on a regime of one pill a day.
"At least it spares me some of the boredom of being a cancer patient because what I’m going through is very absorbing and positively inspiring," he said.
"But if it doesn’t work, I don’t know what they could try next."
He remains hopeful, although he has been told that of 1,000 men of his age and in his condition, half could expect to be dead within a year.
Hitchens said that he is constantly contacted by other atheists telling him he can beat the cancer and this in itself makes him feel "alarmed to be a repository of other people's hope".
People have even started asking him to officiate at their weddings.
"It started a couple of years ago," he said.
"It’s something I shall have to resist if I survive, and even if I don’t – this very slightly cultish stuff starts to happen.
"You get letters from people you can hardly remember meeting: “I shall never forget the kindness …
"Unbelievably trivial stuff, but they’ve made it into a thing in their minds."
