A Nobel Prize-winning scientist says it could be tougher than first thought to harness the healing power of stem cells in medicine.
It had been hoped a single "master" cell could potentially be used to repair all damage in a single organ.
Professor Mario Capecchi, from the University of Utah, found surprising clues that different stem cells might be working together in the same organ.
This means experimental treatments relying on the wrong type might fail.
Professor Capecchi, writing in the Nature Genetics, said the finding suggested stem cell biology could be "more complicated" than previously thought, which could be bad news for patients hoping for the swift arrival of new therapies.
Unlike the majority of cells in the body, stem cells have special qualities.
They not only reproduce themselves, but can produce a wide variety of the cells needed in different parts of the body.
In their most potent form, in the embryo, they have the ability to create any tissue in the body, but cells with more limited, but still useful, abilities have been found in the organs of adults.
Some scientists believe that if these "adult stem cells" could be found and extracted, they could form the basis of treatments, without the controversy surrounding the use of embryos.
However, Professor Capecchi's work means that identifying the most useful cells will not necessarily be straightforward.
He developed a new way of tracking the position of adult stem cells in the intestines of mice.
Unexpectedly, however, he found the cells not spread evenly through the organ, but clustered mostly in the upper third of the intestine.
This means, he said, that other stem cells were likely to be at work renewing tissues elsewhere in the gut.
The most obvious candidate so far is a different variety of stem cell, found throughout the intestine by British and Dutch researchers last year.
One of the researchers, Dr Nick Barker, said that it was possible that the Capecchi cells acted as the "back-up" when these were depleted through injury or illness.
Professor Capecchi stressed the need to pick the right stem cell variety when considering therapy.
He said: "People always thought about a uniform stem cell population in each organ, but now we are saying there are multiple stem cell populations in a given organ, so if you're going to do therapy, you have to recognise this complexity.
"It's important because people are talking about stem cell therapy, they want to stick in stem cells to treat disease."
He said that there was no reason why it should be different in other organs under investigation.
Professor Robin Lovell-Badge, a stem cell specialist from the Medical Research Council, said the finding fitted with other evidence suggesting the presence of different stem cell types.
"This says we actually have two populations of stem cells in the same organ."
He said: "I can see no reason why this also won't be the case in other parts of the body, such as the central nervous system.
"It's important that we find out which is the most useful cell in these organs, if we want to use them in therapies."