It is unclear how he gained access to the house on Knowle Avenue, Ashton under Lyne, at about 3am today but police are warning people to make sure their home is secure and valuables kept out of sight at night.
The man fled when the alarm was raised.
Det Insp Ged O'Connor said: "The man's motives are not clear at this stage in our inquiries, but the family has been shocked by his presence."
The description police have is that he is 5ft 5in tall, of slim build and was wearing a black hooded top and black trousers with a white stripe on the side.
Anyone with information should contact police on 0161 856 9254 or Crimestoppers anonymously on 0800 555 111.
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