Over the coming months 100 hospitals will be subjected to a random, unannounced spot check by the Healthcare Commission.
The findings will be published in the autumn with the dirtiest hospitals named and shamed.
Wards, outpatient areas and accident and emergency departments will all be subject to scrutiny.
Chief executives have been instructed to tell their staff to co-operate with the inspectors who will examine everything from the floors to the state of the sinks and toilets.
Hospitals will be given the results within a matter of days so they can set up actions plans for improvement. Those who perform badly will be checked again.
Anna Walker, the commission's chief executive, said: "Patients and the public tell us they are concerned about cleanliness. There is a real danger this issue could damage confidence in healthcare.
"But there is a shortage of facts and this exercise is about getting those facts. That is why we will be sending in our inspectors over the summer. Our aim is to learn from best practice and challenge bad practice."
A likely contender to be in the spotlight is Brighton and Hove's Royal Sussex County Hospital (RSCH), which was recently revealed to have the third highest MRSA rate in England and Wales with 129 reported cases between April 2004 and March 2005 - an increase of 22 on the year before.
Grandmother and mother-of-two Jean White, 58, of Seaside Avenue, Lancing, said she was appalled at the state of the RSCH and hopes it will be chosen for inspection.
She said: "I certainly think the hospital needs a visit. The food trays were dirty and the showers and bathrooms were filthy. It was not a very nice experience and I would not want to go back to the same ward again."
She said she had seen mould growing on the shower and people using the bathroom could be seen by other patients because the gap between the door and the wall was so big.
Mrs White said: "If the hospital knows it could face inspection maybe it will try to fix some of these problems."
Rosemary Shepherd, chairwoman of Brighton and Sussex University Hospitals Trust independent patient and public involvement forum (PPIF), welcomed news of the visits.
The PPIF already has the power to inspect hospitals and is planning to visit the RSCH on July 20. Mrs Shepherd hopes to see an improvement since their inspection last December.
She said: "At the moment we have to give about three weeks notice before we visit so if they are completely unannounced it will be very effective.
"We have had a lot of feedback from patients at the RSCH who almost all comment that the place is really not adequately clean.
"The beds are so close together and shoved into the corner it is hard to clean behind the properly."
A spokeswoman from the RSCH said the hospital is already subject to scores of checks each year from bodies including local councils, the Commission for Health Improvement, the National Patient Safety Agency and Surrey and Sussex Strategic Health Authority.
Alison Robertson, the trust's director of nursing, said: "We have old buildings and not a lot of storage space so it means a lot of equipment can be out on show in a ward as there is nowhere else for it to go.
"We have set up campaigns like Dump the Junk which encourages ward staff to get rid of equipment they don't use anymore and a Clean and Tidy campaign which works to try and improve the overall impression of a ward."
The trust also has ward housekeepers responsible for keeping areas clean and tidy and modern matrons responsible for checking areas to see if they are up to standard.
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