AS-levels raised fears of exam overload
And they are warning that unless the new qualifications are valued in university applications, students will have little incentive to take the exams.
A survey from the Secondary Heads Association has found that the "great majority of university departments give no credit for added breadth in the courses taken by applicants".
AS-levels, taken in the first year of sixth form, have been introduced in an attempt to broaden the curriculum beyond the traditional A-levels.
But the head teachers' union says that this expansion will be undermined if universities only base their offers on A-levels.
John Dunford, general secretary of the Secondary Heads Association, has written to the Higher Education Minister, Margaret Hodge, warning that students need to see a benefit from a wider curriculum.
And he has called on her to take a lead in urging universities to look beyond the traditional A-levels when offering places.
'Appalling'
"At present schools are encouraging young people to take four or more subjects at AS with little or no evidence that this breadth of study will receive any acknowledgement whatsoever in university admissions offers," Mr Dunford has told the minister.
The union has also described as "appalling" the confusion facing students as to whether their AS-levels will be taken into account by individual universities.
The introduction of AS-levels saw widespread claims that students were facing an overload of exam pressures, with GCSEs, AS-levels and A-levels all in consecutive years.
And if schools discover that the new exams are not being taken seriously by universities, head teachers say they will have little incentive to encourage students to stretch beyond three subjects at A-level.