The proportion of GCSEs awarded a C or higher has risen for the first time in three years, but English results saw their biggest fall in decades.
As teenagers received their grades, headteachers said some schools were seeing "volatility" in results, warning that for some students, this could put their chances of a place at a top university such as Oxford or Cambridge, or their opportunity to go on to sixth-form college, at risk.
Results for England, Wales and Northern Ireland showed a sharp drop in English grades, with 61.7% of entries scoring A*-C, down 1.9 percentage points from last summer.
This is believed to be the biggest drop in the qualification's history.
Maths saw an opposite result, with 62.4% of entries gaining an A*-C grade, up a massive 4.8 percentage points on 2013.
Exam chiefs suggested that the changes in results were down to recent education reforms, including removing speaking and listening from final English grades, a decision that in England, only a teenager's first attempt at an exam would count in school league tables - a move which has hit early and multiple entries - less coursework and a switch by some students to take International GCSEs (IGCSE) in some subjects.
Overall, just over two-thirds (68.8%) of all entries scored A*-C, up 0.7 percentage points on last summer, according to statistics published by the Joint Council for Qualifications (JCQ).
But the A*-G pass rate has fallen for the second year running, and is down 0.3 percentage points to 98.5% from 98.8% in 2013.
The proportion of entries awarded the highest grade has also fallen slightly, with 6.7% gaining an A*, down from 6.8% last year. It is the third year in a row that this has dropped.
Brian Lightman, general secretary of the Association of School and College Leaders (ASCL), which represents many secondary school leaders, said: "We're seeing some surprising results which have shocked some schools.
"They don't understand why, with the same teachers and a similar cohort, and they thought, adapting to the changes that had been announced, that's happened."
Some students have received "shock results" which do not reflect their teachers' assessments of their abilities, he said.
"National statistics do not tell the story of an individual young person who has got a grade, and it may be a D rather than a C, or it may be an A rather than an A*, and remember that could mean Oxbridge or not, or Russell Group or not."
For others it could have an impact on their sixth-form studies.
Russell Hobby, general secretary of the National Association of Head Teachers (NAHT), said: "Many schools have seen unexpected dips in their results, especially in English, with some reports of 20% dips in outcomes. It is great to have this level of transparency but we remain concerned about the factors creating such uncertainty."
"It seems to be schools with a larger number of disadvantaged students, who are working at the C/D border line, that have been hit the hardest," Mr Lightman said.
"It is likely that these students will have struggled more with the move to linear exams and will be disadvantaged by the removal of speaking and listening grades in English."
The removal of speaking and listening is likely to have had an impact particularly because it was seen by some to help students on the C/D grade boundary to get a higher result.
"If you look at the overall results, where speaking and listening is no longer contributing to the grade, it was always our view that would have more of an impact at the C/D borderline," Andrew Hall, chief executive of the AQA exam board, said.
JCQ said the fall in English grades could also be down to strong candidates taking advantage of a final opportunity to sit the exam last winter, and a switch by students to take an International GCSE in the subject.
Mr Hall suggested that the move to "first result counts" has had the most significant impact on entry patterns, and therefore results this year, dwarfing the impact of other changes.
This decision has meant that fewer lower-performing 15-year-olds are taking maths GCSE early, and bright students, who may have taken the qualification early in the past, are now sitting it in the summer, JCQ said.
In recent years there had been a growing trend towards schools entering pupils for exams early, or multiple times, but the new rule has changed this, and new figures published today showed almost a 40% drop in early entry across all subjects.
"What I think is really of note is the change in the 15-year-old results overall," Mr Hall said. "What is driving that is the 'first result counts'. Only the students who are really strong in the school's judgment are being entered at 15, whereas before they were being entered to see how they get on."
In an open letter to schools and colleges, JCQ said those institutions that had traditionally made use of the winter exam season, entered pupils early, or made greater use of resitting are likely to have seen the greatest changes in results this year.
And in a briefing document, exams regulator Ofqual noted that it said last year that when speaking and listening was not part of overall English grades, grade boundaries "might have to be set a mark or two lower than in previous years, in order that this year's cohort was not disadvantaged".
The regulator added that according to its initial analysis, there is more variation this year in schools at grade C in English and English language than in other subjects.
Schools Reform Minister Nick Gibb said: "An exams system had developed that worked against the best efforts of teachers and the best interests of pupils. These results show our plan for education is correcting that. The number of children now taking exams at the right time, the number studying for academic GCSEs and the higher standards achieved are hugely encouraging."