It was not known last night how the boy and girl, both aged under five, died.
Officers sealed off a detached house in the town of Heathfield, East Sussex, where the silver Nissan hatchback in which the bodies were found had been left.
Neighbours said a couple had lived together at the house with two young children. They are believed to have put the house on the market before Christmas after separating. A sold sign is still posted outside.
The woman, believed to be from Surrey, but with local connections, walked into Heathfield Police station close to the house just after 11am yesterday.
It is thought she was taken to Eastbourne District General Hospital under police guard.
Officers forced open the Nissan in Mill Close at 11:46am and made the horrific discovery.
Neighbour Jill Radford, 61, said: "I heard the couple separated just before Christmas and put the house up for sale. It is desperately sad."