The numbers entering for English literature were up more than 10,000 to just over 500,000.
Entries for physics, chemistry and biology also increased by 2 per cent. Exam grades for those taking separate sciences were also well up on the general science grades.
Overall entries for business studies, home economics and art were all down.
Science teachers welcomed the trend, and said traditional separate subjects were a better preparation for A-level than the "double award" general science courses followed by the vast majority of teenagers.
But headteachers insisted that the double award exam - which takes in all three sciences and is worth two GCSEs - had encouraged more girls to go into science.
John Dunford, general secretary of the Secondary Heads Association, said schools were increasing the emphasis on the compulsory core curriculum, which tended to squeeze optional subjects such as art and geography.
Among the optional courses English literature was by far the most popular, followed by French, geography, history, art and German.
Greek was the least favoured subject, attracting just 928 entries, with classical civilisation, economics and Latin sharing space at the bottom of the table.
There was a 16 per cent increase in entries for "short-course" GCSEs, which are taught on a restricted timetable, although much of the increase was made up of candidates taking religious studies or information technology, both of which must be taught by law.
Other short-course subjects attracted only small numbers of teenagers.
Rebecca Edwards, chairman of the Association for Science Education, said: "We are delighted if more young people are taking single subject sciences because it indicates an interest in science and a desire to take it further. It's important for everyone to have a thorough grounding in science and double award science does that very well.
"Separate sciences are a better preparation for A-level, but they have to be taught as part of a balanced curriculum."
Mr Dunford said: "Most comprehensive schools would do double awards science automatically. Getting away from separate sciences has meant far more girls do physical sciences, which offer far more job opportunities. I hope there will be no slide back to single science because it will be bad news in terms of girls doing science.
"About 80 per cent of those doing English are also doing English literature, which means teachers now have more confidence putting their weaker sets in for the exam."
The figures also show the expansion of the pilot of part one General National Vocational Qualifications (GNVQs) which are intended to offer a work- related alternative to GCSEs and which will generally be available from next year.
This year, they were taken by 17,459 candidates in subjects such as business, health and social care and leisure and tourism - up by nearly 70 per cent on last year. The proportion of candidates successfully completing the qualification at foundation level, equivalent to GCSE grades D to G, rose by 1.8 per cent, but the proportion getting an intermediate level, equivalent to top GCSE grades, fell by 2.5 per cent.Reuse content