The hearing is expected to last at least three months. If approved, work on the new line and associated station redevelopments is scheduled to begin in early 2002 and will last for more than four years.
The inquiry will be the largest to be conducted under the Transport and Works Act of 1993, which cuts out the protracted parliamentary procedures followed by major transport infrastructure schemes in the past, such as the Channel Tunnel Rail Link.
The DETR has already received 180 written submissions to the inquiry.
The scheme is proposed by Railtrack and its regulator, the Strategic Rail Authority. It is backed by an ad hoc consortium that includes 140 local authorities, regional development agencies, chambers of commerce and private businesses.
Objections are likely to be concentrated in central London, where businesses in the Borough Market area will be disrupted. The Corporation of London is also expected to object to the proposed closure of the Moorgate rail line.
The aim of the new line is to increase the number of trains that can travel into and through central London. At present, London's rail network can carry eight trains an hour. The Thameslink upgrade will increase this to 24. The trains will also have more carriages.
South of the capital, links with Brighton, Ashford and Guildford will be improved; in the north, King's Lynn and Peterborough will benefit.
The major station revamps will take place in central London. Those affected include Blackfriars Station and bridge, to be designed by Alsop & Störmer; Farringdon Station, by Tony Meadows Associates; an enlarged viaduct across Borough Market, by Terry Farrell & Partners; and a low-level station below St Pancras Station, by Pascall & Watson.
Alongside these projects is the proposed £400m redevelopment of London Bridge Station, to be designed by TP Bennett. Southwark council's planning committee will look at TP Bennett's design before June. Outstanding transport matters, such as the integration of the new rail services with the bus system, are likely to be included in the Thameslink inquiry.
Forty-three outer London stations will have their platforms lengthened to cope with enlarged trains.
Railtrack plans to raise the funds for the project from its balance sheet and the capital market, and recoup the investment from franchising lines to the train operating companies.
Janet Goodland, Railtrack's London director, said: "Thameslink 2000 will reduce overcrowding in the network and connect areas in central London. It will also stimulate the regeneration of rundown areas such as Southwark, Bermondsey, Luton and Dunstable."