The two dresses were due to be auctioned as part of charity events later this year and next in London and New York to raise money for The Amy Winehouse Foundation, which funds a number of concerns including children's hospices and drug counseling.
One of the Back to Black singer's stolen frocks was the dress she wore to marry Blake Fielder-Civil in 2007 and the other was a newsprint cocktail dress. Both were taken from a cupboard in her house after they had been catalogued alongside other items.
The foundation said the house had not been broken into and that a formal complaint to police was forthcoming.
The workers who catalogued the dresses after Winehouse's death had packed them away in a cupboard and discovered two were missing when they later returned to check on the wardrobe.
"It's got to be someone with access to the house," a spokesman for the foundation said.
Amy's father Mitch Winehouse was quoted in London's Evening Standard newspaper as saying that he was "baffled" why thieves had not gone for her designer dresses.
"It's sickening that someone would steal something in the knowledge of its sentimental value," he said.
Amy Winehouse was found dead in her London home on July 23, 2011, at the age of 27 from what officials later determined was accidental alcohol poisoning. There were no illicit drugs in her system.
Fielder-Civil and Winehouse had a turbulent relationship, punctuated by violent fights and reports of heavy use of cocaine, heroin and ecstasy. They were married for about two years until 2009. He also served six months in prison stemming from an 2007 assault on a London pub landlord.
The "Rehab" singer's ex-husband was put on life support in a British hospital in August after an apparent drink and drug binge.
Winehouse's family have said that their daughter beat her drug dependency about three years before her death.
(Reporting by Paul Casciato, editing by Jill Serjeant and Patricia Reaney)
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