Nearly 6,000 British prisoners have low IQs, according to new research by the University of Liverpool on behalf of the Prison Reform Trust (PRT).
Inmates in Liverpool, Styal and Hindley took part in the study
Inmates at Liverpool men's prison, Styal women's prison in Cheshire, and a young offenders' prison in Hindley, near Wigan, took part in the survey.
Projected figures showed that a quarter of British prisoners have an IQ of less than 80 - the national average is 100.
The charity said the research indicated a "vast hidden problem".
PRT director Juliet Lyon said: "This research reveals for the first time that high numbers of people with learning disabilities and difficulties are held behind bars.
"It raises important questions about how they got caught up in the criminal justice system in the first place and whether those responsible for special education, social care and family support could have done more to prevent this".
She added that those with learning difficulties and disabilities in the criminal justice system were "left to wander between police station, court and prison."
The research has been released ahead of the launch in March of "No One Knows", a new UK-wide programme of work to investigate and improve the treatment of people with learning disabilities and difficulties in the criminal justice system.
Author Dr Pat Mottram said: "Overall our findings show that the average IQ of the prison population is 13 below the national average of 100.
"Many will struggle to make sense of their experience of imprisonment", she added.
Skills Minister Phil Hope welcomed the research, saying the government had set in motion major reforms of education for prisoners.