Government spending watchdog, the National Audit Office, is to investigate a £6.2bn programme to install a computer system at the NHS.
Every patient is expected to have an individual record by 2010
The study will assess how the system was chosen and whether it offers value for money.
The system is designed to link every GP's surgery and hospital in England and provide online records for up to 50 million patients.
The government hopes every patient will have their own online record by 2010.
But NHS IT director general Richard Granger says people will start to feel the benefits of the system by 2005.
According to health officials, the system will allow information about patients to be mobile for the first time.
As a result, a wide range of organisations will gain access to records previously kept in one place.
But doctors fear patient confidentiality could be jeopardised.
And at the British Medical Association's local medical committee conference in June, GPs voted against backing the system until their uncertainties had been addressed.
The National Audit Office's study will assess the overall design of the system, whether there is enough money for training, the cost of local implementations and whether doctors will support it.
A spokesperson told Computer Weekly magazine: "It is to be expected such an important programme will be the subject of an NAO report to Parliament.
"The fact we are starting work does not imply any particular concern with the way the programme is going.
"We are starting now because it appears to us that, with the letting of the major contracts and the beginning of the inevitably long process of implementation, it is a good moment for Parliament to be given a stocktake and a forward look."
The NHS has welcomed the NAO's intervention.
A spokesman added: "It is only natural, and it has always been expected, that such an important programme should be the subject of an NAO report.
"Having largely completed our procurement phase and being well into initial implementation, this is naturally an appropriate time for such a report to be done and we welcome it," he said.
The NAO is expected to issue a report on the scheme to the government next summer.
Paul Burstow, Liberal Democrat health spokesman, said: "There are huge risks involved in this IT project.
"Ministers must learn the lessons from past mistakes and deliver the project on time, on budget and fit for purpose.
"The government owes it to patients and staff to get this right."
Dr John Williams, an IT spokesman for the Royal College of General Practitioners, welcomed the investigation.
He said: "Given this is the largest IT project in the history of the NHS, and in view of problems with NHS IT systems in the past, this investigation seems highly appropriate.
"Apart from the tendency for such projects to over run and over spend, GPs are worried about the safe transfer of patient records to the new national computer system.
"If you want technology to deliver you need the people and organisational systems in place to implement it."