RSS feedsThe study by Westminster's main financial wathdog 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 with any doctor in the NHS able to access patient records immediately when necessary.
THe NAO has decided to look at the scheme now after the letting of the main contracts rather than wait seven years till it is completed or for problems to surface.
Doctors have expressed fears over patient confidentiality 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 NAO'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 spokesman said: '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.'
The NAO is expected to issue a report on the scheme to the government next summer.
