I think "transversal" is one of those words that means different things in different places. In Spain, as Noni has said, it is a kind of "buzzword" in education and means cross-curricular or multidisplinary: cutting across subject boundaries. It probably means this in Latin America too.

However, here I think it probably means something different. Since you are in Chile, María Eugenia, the context may well be Chilean. The subject of "exámenes transversales" at university level is discussed in a number of Chilean sites, and generally, if not always, in relation to the DUOC UC (Dirección de Desarrollo Curricular - Universidad Católica), a multi-campus institution with thirteen "sedes" across the country, from Alameda to Valparaíso:
http://www.duoc.cl/sedes.html

The reference here to the Unidad Tecnológica Educativa suggests that it probably is referring to DUOC UC, which has an UTED on each campus; see for example http://www.duoc.cl/info2/367/n30.html .

Unfortunately, the main DUOC documents on exámenes transversales are not on open access; you have to be registered. However, the site’s glossary offers this definition:

“Examen Transversal (ET)
Es una instancia en la que se recoge información sobre el desempeño de un estudiante con respecto a las competencias y unidades de competencias asociadas a una misma asignatura y/o módulo a partir de evidencias específicas.
Los exámenes transversales se aplican al término del período lectivo en el período dispuesto en el calendario anual como “período de examen” y se extiende a las distintas sedes donde se dicta la asignatura y/o módulo y al total de secciones de la misma. [...]”
http://www.duoc.cl/ddc/glosario.php

I think the highlighted phrase gives us the vital clue: “exámenes transversales” are exams set and taken by all the DUOC UC campuses where a given subject is taught, as opposed to the usual exams set and graded by the course teacher on a single campus.

This is confirmed by the following comment:

“Por otro lado los famosos examenes transversales que según ellos es para que en ese día todas las sedes que imparten ramos de construccion tengan el examen que los hace otros profesores y que no tienen nada que con las materias pasadas en el semestre y entonce esos examenes son todos malas notas y por ende casi reprobacion de ramos.”
http://www.reclamos.cl/reclamo/2008/dec/duoc_uc_no_respetan_...

This echoes a common complaint among DUOC students: they find that the exámenes transversales contain material they have not covered, and they blame their own teachers for failing to cover the syllabus properly.

So I think we are talking here about national examinations in this particular institution. You could perhaps call them “cross-campus examinations”. This expression is rare, but I’ve found one example from the University of Durham in the UK:

“Cross-campus Examinations
Noted: that the Department of Psychology operate some cross-campus modules and it would be helpful for them if some examinations could be co-timetabled at Durham and Queen’s Campus, Stockton.”
http://www.dur.ac.uk/committees/Faculty-of-Science-SubCommit...



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Note added at 13 hrs (2012-01-29 15:28:40 GMT)
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This idea of being examined by people outside your own college or campus is an important educational issue in itself; it is inherently more testing for the students, and may be regarded as more objective: they are being evaluated by people who don't know them at all. This is the case with A Levels in Britain, for example, which are national, as opposed to the Bachillerato in Spain, where the result depends entirely on the class teacher's assessment. It also constitutes a test of the teacher, since the results achieved by his/her pupils can be seen as a test of his/her own teaching. This, I think, is why these "exámenes transversales" help to "medir la eficiencia de los métodos pedagógicos", as the context says. When the students are taught and assessed solely by the course teacher (as usually happens), no such external check exists.

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Note added at 14 hrs (2012-01-29 16:21:27 GMT)
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Note also, by the way, that if the DUOC's definition applies here, these exams are neither cross-disciplinary nor comprehensive. They are examinations on particular "asignaturas" or "módulos", taken by students studying the asignatura/module at all the different campuses.

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Note added at 1 day7 hrs (2012-01-30 09:05:21 GMT)
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That's great, María Eugenia, I'm very glad. I thought it must be this DuocUC thing. Just an afterthought on what to call it in English: maybe "national" is too general a term, since these exams are held within this particular institution rather than nationwide. "Cross-campus" is probably better, though maybe it could be misinterpreted as referring to exams held across a particular campus. I wonder whether "multi-campus" could be used here, to make it completely clear. DuocUC is what you could call a multi-campus university, so it makes sense, I think.

Here's an example of the term:

"The little corporations could be very small, say two or three friends selling their services to the Modern Language Department to teach beginning French or Spanish, or could be huge, selling services university-wide. In the long run, larger companies will try to buy up the smaller firms and try to achieve some economies of scales. How that would work out is unknown, because I am uncertain as to the scale economies realizable here, but I suspect they are sizable (e.g., developing a common curriculum usable on many campuses, offering common multi-campus exams, perhaps have some lectures provided at multiple campuses simultaneously using distance learning techniques)."
http://centerforcollegeaffordability.org/archives/329

Maybe the word "common" would go well here too.