Jakob von Gunten (Mark Rylance) arrives to enrol at a secluded, mysterious academy for servants, called the Institute Benjamenta. Decorated throughout with images of deer, the school is run by brother and sister Johannes and Lisa Benjamenta (Gottfried John and Alice Krige). There are eight other students, of which Kraus (Daniel Smith) seems to be favourite. Jakob participates in bizarre ritualistic lessons which appear to revolve around cutlery and napkin-folding, and gradually finds himself favoured by the proprietors. Eventually he uncovers the brooding secrets that lay at the heart of the Institute.

Seem, appear...the first investigation by the Brothers Quay into features is, like their celebrated animations, full of words about chance and possibility. Here are 105 minutes, of which none are absolute, nothing fixed. Like early David Lynch (it's reminiscent of The Grandmother and even Eraserhead) or the live-action/animations of the great Jan Svankmajer, it makes demands of its audience as translators. No one is relaxed into a story, a sequence of clearly delineated events. Its images provide its meaning rather than support it.

This is, of course, both the film's saving grace and its downfall. For sure, the images the brothers (Americans resident here for many years) conjure are remarkable: the proliferation of the deer motif, circles/zeroes, mirrors, ice, forks, buckets of water sluicing through floorboards and down walls. They cut-in brief animated passages, and concentrate perhaps more than any other film-makers on the import of the close-up. Objects both huge and minute are placed on a par by their framing and unfamiliar angles. The move is to disorientate on both scales.

The script, developed from Robert Walser's novel Jakob von Gunten by the brothers and Alan Passes, has a strong fairytale ring. Occasionally the film resembles a very dark, very adult kind of a pantomime. The humour is especially dry. At times it serves to roll-call names from the avant-garde: the Coens (Barton Fink, in particular); Peter Greenaway; Philip Ridley; Denmark's Lars von Trier; even Roger Corman's marvellous Poe movies. The closing death scenes are Cocteau's La Belle et la Bete, while much of the rest recalls nothing so much as Guy Maddin's bewildering Careful.

Much of the playing is inevitably puppet-like, with only really the delicate Krige instilling any emotional depth. Her increasing breakdown in control and composure focuses the eye. In the absence of character, much is left to music, and Lech Jankowski's score is the film's one unqualified triumph. From angelic chorus to acoustic guitar to (memorably) Miles Davis-esque trumpet and occasional Free Jazz sax squall, it counterpoints on-screen events with rare precision.

The film doesn't always work by any means (outstaying its welcome by a good twenty minutes, the opening being especially tedious) but when it fuses, something singular, new even, appears on screen: the web-like gallery that Lisa takes Jakob to visit; the classroom ceremonials; the funeral; water spilling in silver ribbons. It becomes a series - a list - of brilliant shorts strung together to feature length. Timothy and Stephen Quay clearly have much to learn about real people and about real pacing, but much of their film is quite mesmerising and occasionally truly magical.