For the Neue Synagoge in Heidelberg, conceived and fabricated between 1993 and 1994, Brian Clarke designed ten six-metre-high stained glass windows and a mosaic artwork for the Torah shrine. The building was created by architect Alfred Jacoby, with whom Clarke had first collaborated in 1988 for the Holocaust Memorial Synagogue in Darmstadt.

In his 1994 essay ‘Architectural Artist’ from the eponymous monograph on Clarke, Kenneth Powell writes:

‘The Heidelberg Synagogue led Clarke to experiment with new glass making techniques. Clarke talks of the "intellectual ping-pong game" which he plays: on one side is his painting, on the other his architectural art. Watercolour is a medium which Clarke uses relatively rarely (he used it when working up his designs for the Future Systems Hamburg scheme). Its special qualities might seem peripheral to the matter of stained glass design. For the Heidelberg commission - ten windows, each six metres high - Clarke actually dispensed with conventional leading. He had the idea of "pools" of watercolour piercing areas of solid blue colour (the effect provided enormous difficulties for Clarke's manufacturer, Mayers of Munich). Clarke also wished to incorporate panels of Hebrew texts into the glass, a technique familiar to the Victorians but unusual in modern glass.’