DNA samples are taken from about 22 children a week in South Yorkshire, according to newly-released figures.
Swabs were taken from 1,146 boys and girls aged 17 or under during 2011 – including 30 primary schoolage children.
Across England and Wales, police took swabs from almost 54,000 youngsters that year, while in 2010 almost 70,000 samples were taken.
Under current rules, police can retain indefinitely the DNA of anyone they arrest for a recordable offence.
A new law, imposing tighter restrictions on DNA retention, is expected to come into force later this year.
Frances Crook, chief executive of the Howard League for Penal Reform, said: “When public money is tight and police forces are shrinking, it is disappointing to see valuable crime-fighting resources being wasted on taking DNA samples from thousands of innocent children, while serious offences go undetected.
“Children who get into trouble with the police are usually just up to mischief.
“Treating so many like hardened criminals by taking their DNA seems excessive.
“We welcome the government’s decision to stop storing innocent people’s DNA indefinitely, but it remains unclear how this will affect the number of children having their DNA taken needlessly.”