Figures released on Wednesday show that Guy's and St Thomas's hospitals had the highest MRSA rates of any specialist trust in the country at 0.45 per 1,000 bed days.
166 cases of the so-called superbug were reported at SE1's two hospitals last year.
The Department of Health said that there were difficulties in comparing rates with different trusts because of factors such as the types of patients treated at different hospitals.
'Today's publication of the latest MRSA rates, hospital by hospital, on the internet is an important part of giving patients more information about this problem," said health secretary John Reid.
"It is clear from these figures, and from today's National Audit Office report, that some parts of the NHS have to do more to control this threat and match the achievements of hospitals which maintain low MRSA rates.
"The NAO report is an important reminder that everyone in the NHS needs to keep infection control at the top of their agenda."