Almost 40% of children who visit their GPs with persistent coughs have signs of whooping cough, a study suggests.
Babies are vaccinated against whooping cough
The University of Oxford researchers said its research, which involved 172 children, showed whooping cough was widespread among young children.
Children are immunised against the disease as babies and before school.
But the team says its study - reported in the British Medical Journal - shows GPs should consider diagnosing whooping cough even in fully immunised children.
The number of cases of whooping cough has fallen substantially over the past 20 years.
But Health Protection Agency figures show a rise in the last year in the number of younger children diagnosed with the condition.
In 2004, there were 237 cases among children aged four and under, rising to 289 in 2005.
Neither infection nor immunisation with the pertussis jab currently used gives lifelong immunity.
But the researchers say GPs tend to view whooping cough as only affecting very young children who have not been immunised and who have classic features such as whoop.
Their study looked at 172 children aged five to 16 years of age who visited their family doctor with a cough which had lasted at least 14 days.
The length of time they had been affected by the cough, and how severe it was, were recorded, and the child's immunisation records checked.
Blood samples were taken to test for pertussis infection and parents and children also completed a cough diary.
The researchers found that 64 (37.2%) children had evidence of a recent pertussis infection. Fifty-five (85.9%) of them had been fully immunised.
Children with pertussis were more likely than others to have whooping, vomiting, and sputum production.
They were also more likely to still be coughing two months after the start of their illness, continue to have more than five coughing episodes per day, and cause sleep disturbance for their parents.
Dr Anthony Harnden, an Oxford University lecturer and GP in Oxfordshire, who led the research, said the vaccination policy did work.
"The immunisation is very effective - we know that because very few infants die of whooping cough.
"But what the immunisation does not do is last for a long time."
He added: "Our main message is that doctors should consider a diagnosis of whooping cough even in a fully immunised child."
The children did not receive the pre-school booster which children are now given.
But Dr Hardman said there were still questions.
"There's a debate about whether we should introduce an adolescent booster but that could push it upwards into the parent population, which has its own set of problems. That's the dilemma."
A spokesman for the Health Protection Agency said: "We're fully aware that protection from the vaccine wears off.
"But it's very good at protecting young babies - and they're the ones who can die from whooping cough. So we've built the whole vaccination programme is built around them."
And Dr Graham Archard, vice chairman of the Royal College of General Practitioners, said: "It would be unreasonable to suggest that GPs have been performing at a lower standard that patients may expect.
"Making a diagnosis of whooping cough necessitates uncomfortable blood tests which are usually avoided in young children unless there is clear benefit in undertaking the blood test.
"This new evidence asks many questions of how GPs and other clinicians should be expected to deal with the huge number of children presenting with coughs, of which 40% may have whooping cough."
A spokeswoman for the Department of Health said it was important that children received all their childhood jabs.
"The vaccine is very effective, especially in protecting against severe disease."