Just one in 15 (6.5%) pupils starting secondary school in England "behind" for their age goes on to get five good GCSEs including English and maths, official data shows.
The government data published as part of secondary school league tables suggests the majority of schools are failing struggling pupils.
Nationally 58.2% of pupils reach the five good GCSEs benchmark.
Minister Nick Gibb said schools which let pupils down would be tackled.
The Department for Education data covers England's more than 5,000 secondary schools with more than 200 pieces of information being published for each one - almost four times as much as last year.
Much of the information is broken down by pupil type, with scores offered for low, medium and high-attaining pupils, and those from disadvantaged backgrounds as well as non-disadvantaged.
As expected, those from disadvantaged backgrounds (classed as those on free school meals or in local authority care) do less well.
Only a third (34%) of these children achieve the government's benchmark of five GCSEs - or equivalent qualifications - graded A* to C, including English and maths.
In 909 schools, not one low-attaining pupil (those who did not reach Level 4 at the end of primary school) reached this threshold.
At the other end of the spectrum, 95% of pupils who started school "ahead" for their age (achieving Level 5 at the end of primary school) got five good GCSEs, including English and maths.
And of those who started school at the expected level for their age, (Level 4 at the end of primary school) some 45.6% failed to progress to five good GCSEs.
Overall, 58.2% of pupils in England's state schools got five good GCSEs including English and maths (including equivalent qualifications).
When these qualifications, such as BTecs and NVQs, are excluded, 52.4% of pupils gained five good GCSEs.
The performance data also shows what proportion of pupils get the English Baccalaureate.
This new measure, introduced in 2010, is the proportion of pupils achieving A*-C passes in English, maths, two science subjects, a modern or ancient language, and either history or geography.
Nationally across all pupils, just 15.4% got the wrap-around qualification, but most pupils would have made their GCSE choices before Education Secretary Michael Gove announced he was introducing this certificate of achievement.
Pupils with low prior attainment also performed poorly in the English Bacc, with just 0.3% gaining the wrap-around qualification.
Sevenoaks School, a private school in Kent, tops the English Bacc tables, with 99% of pupils meeting this benchmark.
Schools Minister Nick Gibb said: "Today's figures reveal a shocking waste of talent in many schools across the country. All too often, pupils from disadvantaged backgrounds aren't given the same opportunities as their peers.
"But there are great examples of schools achieving the best for their disadvantaged pupils. If they can get it right, then so can all schools."
The government says its data shows there are 107 secondary schools below the floor standard of 35% of pupils getting five good GCSEs, including English and maths.
Mr Gibb added: "Children only have one chance at education. These tables show which schools are letting children down. We will not hesitate to tackle underperformance in any school, including academies.
"Heads should be striving to make improvements year on year, and we will not let schools coast with mediocre performance."
In total, 158 schools see 100% of pupils getting five GCSEs A*-C or equivalent, including maths and English.
When the average point score per pupil is used to rank these schools, the Lawrence Sheriff Grammar School in Rugby comes top.
Head teacher Dr Peter Kent said much of the school's success was down to Key Stage 4 being spread over three years rather than the traditional two.
"This gives departments a chance to deliver a very personalised curriculum and we all respond well to something that's been tailored to our individual needs," he said.
The poorest performing school was St Aldhelm's Academy in Poole, Dorset, where just 3% of pupils got five GCSEs A*-C or equivalent, including maths and English.
Principal Cheryl Heron, who took over in September 2010, said the results were "disappointing but not unexpected". It would take time to change and transform pupils' learning experiences, she added.
At sixth form level, the Colchester Royal Grammar School in Essex comes out as the best performer, with an average point score per pupil of over 1,477 - this is the equivalent of over four A*s and one A grade at A-level.
The best performing county was Sutton in London, where 74.7% of pupils got the government benchmark of five GCSEs, including maths and English.
The worst performing council was Knowsley, Merseyside, where 40.8% of pupils reached this level.
A spokesman for the council said: "The levels of attainment in Knowsley's schools are improving year on year and we are striving to accelerate that improvement in 2012 and beyond.
"There are areas for improvement and we will continue to focus on bringing all our pupils up to the level of the best."