The dress she wore to marry Blake Fielder-Civil in Miami in 2006 was stolen along with a newsprint cocktail dress she wore to perform on the BBC live music show Later With Jools Holland.
The wedding dress could have raised up to £100,000 for her foundation which helps youngsters beat drugs and develop their music.
And the cocktail dress could have raised a further £30,000 at the auction later this year.
A spokesman for the Amy Winehouse Foundation said the dresses were stolen from the performer’s Camden home in north London but it is not believed the property was broken into.
Winehouse’s family have been cataloguing her possessions at the property – which fans have turned into a shrine – and realised only recently that the garments were missing.
Because of the items’ significance, it is thought they might have been stolen to order by someone entering the property during events after her death in July last year.
The spokesman said: “A lot of clothes and items were left and they were being catalogued when it was realised these two were missing.
“They were going to go to the foundation but somebody might be trying to sell them for their own profit. People need to know they are not supposed to be out there on the market and they should not try to buy them.
Scotland Yard has not received a formal complaint but it is thought the star’s father Mitch Winehouse has been speaking with a family liaison officer assigned to them after his daughter’s death, which stunned the music world.