The move comes after evidence of the disease, which has killed 27 people since May 1995, was found in the appendix of a man who later died of the condition. Tony Barrett, a coastguard, died in hospital in Plymouth last June. His appendix had been removed in Torbay hospital in Devon in September 1995.
If a survey of the samples revealed more cases of new variant CJD - the type linked to BSE - it would raise the possibility of a way to screen the population for the condition.
Estimating the extent to which nvCJD spread before potentially infected beef was removed from the food chain has previously been been impossible, with figures quoted ranging from a few hundred to many thousands. Previously, confirmation was only possible by examining the brain after death.
A spokesman for the Department of Health said the research would be done anonymously on samples previously removed from patients.
He said: "We will do some retrospective research on samples of appendices to see if there are any affected by CJD. We are talking to the Medical Research Council about how this could be conducted. It is in the early stages of research. Mass screening is not on the cards at the moment: there are still several questions to be addressed."
Around 44,000 appendectomies and 800,000 tonsillectomies are carried out each year. Out of a population of 50 million, the number showing signs of CJD is likely to be low.
Sir Kenneth Calman, the Chief Medical Officer, said the exercise would simply provide an idea of the effects of BSE on the population and might not throw up any concrete information. If nothing were revealed, it would not necessarily be reassuring, he said.
Ethical guidelines would have to be drawn up to cover any mass screening system, which would be by taking samples from new patients. They would cover the question of whether individuals should be told of positive results; nvCJD is incurable.