The molecular basis for red/white colour determination in grape berries is known to involve a myb-factor regulating at least the expression of UFGT. This study was performed to further explore co-ordinated gene expression patterns associated with colour determination in grape berries. We have set up a dual screening strategy using both a SSH library construction and 3 K-oligo-arrays- profiling. Two subtractive libraries (SSH) were obtained by comparing two red skinned cultivars with either red (Lacryma) or white pulp (Gamay). The association between gene expression and colour was further evaluated for some positive clones using a red pulp Gamay cultivar (Gamay Fréaux). Microarray profiling was performed in several red/white samples to identify isogenes consistently expressed in red tissues whatever the source of variation (genotype, development, tissue). The expression of a set of nine isogenes was consistently associated with the coloured berry tissues. Four of these isogenes were related to the flavonoid metabolism pathway (chalcone synthase (isogene CHS3), glutathione S-transferase (GST), UFGT, caffeoyl methyl transferase (CaOMT)), two of them (GST and caOMT) being reported and characterized for the first time in grape berries. Our results thus suggest the involvement of upstream (CHS3) and downstream (GST, CaoMT) isogenes of the anthocyanins pathway, in addition to UFGT for the determination of grape berry colour.