Hospitals will be served with "improvement notices" if they fail to tackle MRSA and Clostridium difficile, the health watchdog announced.
Experts from the Healthcare Commission will carry out "spot checks" on 120 NHS trusts in England over the next year.
Those that are not up to scratch could find themselves served with an improvement notice or be put in special measures.
The crackdown comes after figures showed C diff is still on the rise.
Health Protection Agency (HPA) statistics released in April identified 55,681 cases of the potentially fatal bug in patients aged 65 and over in England in 2006. That figure was up 8% on the number of cases reported in 2005.
MRSA bloodstream infection figures revealed 1,542 cases in England between October and December 2006, down 7% on the previous quarter.
Despite the fall, the Government is widely expected to miss its target of halving rates of MRSA before April next year.
The Healthcare Commission will use existing data on infection rates and cleanliness to identify trusts that may need help.
Those not doing well will be prioritised but up to two thirds of NHS acute trusts will be checked each year as part of the programme.
Their performance will be assessed against the Government's "hygiene code", which sets out 11 compulsory duties to prevent and cope with hospital superbugs.
Read More
MORE ABOUT