The proportion of GCSEs scoring a C or above has fallen for the first time in the exam's 24-year history.
Official figures reveal a 0.4% drop in the A*-C pass rate. The results also show that the percentage of entries awarded at least C in the key subjects of English, maths and science has also fallen.
Thursday's national figures reveal that 69.4% of all GCSE exams were given at least a C grade - down from 69.8% last summer. It is the first time that the A*-C pass rate has fallen in the 24-year history of GCSEs. The exams were first taught in 1986, with the first exams taken in 1988. Around 650,000 in England, Wales and Northern Ireland received their results.
Exam board chiefs said this had been a year of "major change" and that drops in results were partly down to tougher science GCSEs and more candidates sitting English in the summer rather than earlier, in the winter exam season.
The Joint Council for Qualifications, which publishes the national results, said there had been a "dramatic" increase in entries for science GCSE - up 36.5% - and said that the fall in results at A*-C in this subject is partly due to a "more demanding standard" introduced this year, and a "significant" increase in entries by 15-year-olds.
Andrew Hall, chief executive of exam board AQA, said: "This year has got more change in it than I think I've seen in my time at any awarding body." AQA stressed that the standards students have to achieve remained the same.
Ziggy Liaquat, managing director of Edexcel, said: "The quality of work required to achieve an A grade this year is the same as the quality of work required to achieve an A grade last year."
The exam boards said changes were most apparent in the science results, with Mark Dawe, chief executive of the OCR, saying that the Government wanted a more difficult paper set for students.
Education Secretary Michael Gove said the reason some pupils have had poorer results than expected was partly down to a change in the system which meant their exams had been split into units and modules this year. He insisted that the decision to change the grade boundaries was down to individual exam boards and was "fairly comparable" with previous years.
Asked about concerns from English teachers that exams in their subject have been marked too harshly with many pupils who were expected to get Cs getting Ds, he said: "That is a result of the independent judgments made by exam boards entirely free from any political pressure and I think that the various chief executives of the exam boards, and indeed the chief executive of the regulator Ofqual, have made it clear today that these decisions have been made because the exam boards and the regulator have sought to ensure this year as every year, that exam results are comparable over time so that we can all have confidence in the examination system."