Prof Sir Michael Marmot said they die 15-20 years earlier than other people due to poor housing, low incomes, social isolation and bullying.
He said 40% of people with learning difficulties were not diagnosed in childhood - and this had to change.
Learning disabilities affect 2.9% of the population.
But a quarter of young people in custody have learning disabilities, the report said.
Prof Marmot, from the Institute of Health Equity at University College London, estimates that shorter life expectancy affects 1,200 children and adults in this vulnerable group, who are also at higher risk of mental illness.
'Less discrimination'
He said more should be done to improve the lives of all children with learning disabilities.

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