Surgeons are being asked to reconsider the methods they use.
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A common procedure for removing tonsils could cause bleeding and complications after surgery, warn experts.
The National Institute for Clinical Excellence, in an interim report on tonsillectomies, said doctors should avoid a procedure called diathermy.
The procedure uses heat generated by an electrical current to remove the tonsils and close the blood vessels up.
The report recommends surgeons use the 'cold steel' method, which does not use heat.
Chief Medical Officers for England, Scotland and Northern Ireland asked NICE to review the types of tonsillectomies conducted by the NHS.
NICE found that diathermy was far more likely to cause bleeding and complications requiring further surgery in patients than in those who had undergone cold steel surgery. Two patients are known to have died after undergoing diathermy.
Common operation
One type of procedure, called monopolar diathermy, was almost five times more likely to cause post-operative bleeding in a patient than a cold steel tonsillectomy, and four times more likely to lead to complications requiring further surgery.
Around 45,000 people undergo tonsillectomies each year. Half of these operations involve the use of heat.
However the report stressed that tonsillectomies are usually safe procedures that go ahead without complications.
NICE Chief Executive, Andrew Dillon, said: "NICE has issued interim guidance as a sensible precaution until the full benefits and risks of these procedures have been assessed.
"We will follow up with a full review and issue definitive guidance as soon as it is complete."
Professor Bruce Campbell, Chairman of the Interventional Procedures Advisory Committee said: "The guidance NICE is releasing means that surgeons are full informed about the risks associated with doing tonsillectomy in different ways, so they can make sure they are providing their patients with the best possible care."
Diathermy has been used increasingly because of fears of transmitting vCJD from reusable surgical instruments.
But the report recommends doctors switch back to using re-usable instruments instead of disposable ones.
It said precautionary action in 2001 to lower the risk of patients contracting vCJD resulted in many surgeons using disposable equipment.
However the report said disposable equipment was linked to a higher rates of surgical complications.
Solicitor Richard Follis, of Alexander Harris Solicitors, is representing the parents of two patients who died after undergoing tonsillectomies in England.
Disposable diathermy instruments were used in both tonsillectomies and both patients suffered serious haemorrhaging after their operation.
He said: "We welcome both the issuing of the guidance today and the involvement of NICE.
"Parents have shown incredible determination applying sustained pressure to the relevant officials for over two and a half years since their children's death.
"They are pleased that the guidelines recognise a serious level of concern surrounding the use of these instruments and is at last the start of the process of answering a whole series of questions that they have.
"We will certainly look forward to seeing the results of their full investigation when available."