The remains, contained in a carved Japanese box, will go on the block in September, 32 years after Capote's death, reported The Guardian.
The starting price is USD 2,000.
"With some celebrities this wouldn't be tasteful, but I know 100 per cent he (Capote) would love it," said Darren Julien, president of Julien's Auctions.
"He loved to create press opportunities and to read his name in the paper. I think he would love it that he's still grabbing headlines today."
The ashes are part of the estate of Joanne Carson, the late wife of former "Tonight Show" host Johnny Carson, who died last year. Carson was a close friend of Capote and hosted him at her Bel-Air mansion, where he died of liver disease in 1984, aged 59.
He said that to his knowledge it was the first time human ashes had been auctioned. "It's never been done. This will be right up there."
Julien added Capote fans and collectors had expressed interest in the ashes and predicted they would fetch a lot more than USD 6,000.
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