Plans to reform A-levels could lead to a two-tier system with students discriminated against because of the subjects they choose, the Government has been warned.
Proposals have been put forward to bring in new style A-levels on a subject by subject basis over a number of years.
But there is a risk that this could mean that some subjects lose value, with "lasting damage" done to those which are not revamped until later on, according to UCAS.
The admissions body also warned that there is a risk that if the new courses are seen as tougher, students could be put off, leading to a fall in demand.
UCAS raises the concerns in its response to Ofqual's consultation on A-level reform.
The consultation put forward proposals to bring in the first new A-level courses for teaching in 2014 in some "priority subjects".
Other courses would then be brought in between 2015 and 2018.
But in its response, UCAS said there is a risk that these "early phase subjects" may be preferred by universities.
This could could create "a two tier situation where some subjects lose value, and students may be discriminated against because of subject choice," it says.
"Were this to be the case, or thought to be so, there may be lasting damage to the popularity of some subjects in these later phases and a potential for negative impact on social mobility."
UCAS also warns: "There is also a risk that if new specifications were perceived to be more "difficult" students would shift subject preferences away from key subjects and demand would fall in important subject areas."
This is what happened to A-level maths as a result of reforms known as Curriculum 2000, it adds.
Speaking at a higher education conference in central London today, UCAS chief executive Mary Curnock Cook, said: "We have reform of A-levels on the table.
"I don't think we know what is actually going to be done yet, but the kind of mood music is tougher A-levels.
"I know Curriculum 2000 was 10 years ago, but have people forgotten that if you make A-levels tougher, you will depress participation and you will depress achievement.
"So if A-levels are still the key currency for progression to HE we just need to have that on our radar screen.
"I'm not against changes to A-level, I'm just stating what I think is a fact."
The Curriculum 2000 reforms led to a "clear and dramatic fall off" in demand for maths A-level, that was then corrected, Curnock Cook said after the conference.
"It was about the perceived difficulty of the A-level and in particular it was about the gap between what was done at Level 2, at GCSE, and the perceived step up to A-level, so I have concerns not only about the headline impact of young people gaining an understanding, either rightly or wrongly, that A-levels have got harder, but I also have concerns about not doing the reforms in step with GCSE, because you have to secure the progression to whatever you're progressing to."
Curnock Cook added that some of the timetables for reform that have been discussed are "highly risky".
"We have history to tell us that if you're doing radical reform and you do it very quickly and you do it without piloting you might well bump up against some unintended consequences," she said.
UCAS' response to Ofqual said that there are "considerable risks to overly-rapid development" of qualifications - and pointed to GCSE science, various maths qualifications, Curriculum 2000 and the Labour government's Diplomas as examples.
The document also says UCAS is interested in the subjects identified for the first wave of A-level reforms.
Ofqual says it thinks it would be a "good option" to begin with a selection from chemistry, physics, biology, mathematics, English literature, geography, history, French, German and Spanish.
These are all subjects preferred by leading Russell Group universities, UCAS says, adding "we would like to understand more about the rationale behind this list which excludes a number of significantly more popular A-level subjects taken by UK candidates."
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