The majority of people having planned operations will now be screened
Most people being admitted to hospital for a planned operation will now be screened for MRSA.
Health Secretary Nicola Sturgeon said national screening would be introduced after a pilot by three health boards.
Attention will be paid to the elderly and people admitted for kidney disease, skin problems and vascular surgery, as the pilots showed higher MRSA rates.
It comes as new figures showed a drop in the number of hospital patients infected with C.difficile and MRSA.
From October to December there were 1,299 cases of C.diff - down 9% on the previous quarter - and a 19% reduction on the same quarter in 2007.
There were 157 MRSA cases, which was up 7% on the previous quarter but down 24% on the same quarter in 2007.
This is the second lowest figure ever, and the lowest of any previous quarter in winter.
Health Protection Scotland (HPS) has published an interim report into the £3.7m pilot screening programmes being conducted in the Western Isles, Grampian and Ayrshire and Arran.
Since June, patients in those areas have been routinely tested for MRSA before being admitted to hospital.
If they tested positive they were given a five-day course of treatment to make sure the bacteria did not get into their bloodstream or carry to other patients.
The HPS report indicated that 7.5% of patients who were screened as part of the pilot carried MRSA harmlessly on their skin.
But as many as 20% of patients who were elderly, or those admitted for kidney disease, surgery on veins and skin problems, carried the bug.
This is why patients in these groups will be targeted in the national screening programme.
Ms Sturgeon said: "We have worked tirelessly to crackdown on these infections which cause misery and worry for patients and their families.
"Our intensive efforts are bearing fruit. But there is more to do if we are to wipe out the scourge of avoidable hospital infections.
"That's why I am announcing today we will roll out a national MRSA screening programme over 2009/2010."