Apple fruit display a wide range of colours from green and yellow through to an array of red shades. The biochemical basis of colour differences in apples was investigated with a particular focus on the flavonoids. Three main groups of flavonoids were found: anthocyanins, flavonols and proanthocyanidins. Apples contained predominantly 3',4'-hydroxylated flavonoids (e.g. cyanidin and quercetin glycosides) with only small amounts of 3'- (e.g. kaempferol glycosides and phloridzin) and 3',4',5'-hydroxylated compounds (e.g. (+)-gallocatechin). Galactosides were generally the predominant flavonoid glycosides and the pattern of glycosylation was a result of either the substrate specificity or the levels of specific glycosyltransferases. Pigment composition was determined for a number of New Zealand-grown apple genotypes and Malus species and differences in flavonoids were found to be quantitative and not qualitative. In addition, there were large differences in the concentrations of chlorophyll and carotenoids. Changes in pigment composition, and the activities of three enzymes of the flavonoid biosynthetic pathway (PAL, CHI and GT) were measured during the development of red and non-red apple fruit. The composition of the flavonoids in red and non-red cultivars was similar except that the red cultivar synthesized cyaniding glycosides during ripening. There were significant quantitative changes in all pigment groups during ripening but there were no significant qualitative changes in flavonoids. There was coordinate regulation of the flavonoid enzymes, including PAL, during both developmental regulation and UV induction of flavonoid biosynthesis. Changes in enzyme activities generally correlated with changes in flavonoid concentration, particularly during ripening, although none of these enzymes appeared to be the rate-limiting step(s) in flavonoid biosynthesis. PAL-IS did not have a significant effect in controlling the changes occurring in flavonoid biosynthesis. Differences in accumulation rates of flavonoids in the two cultivars investigated in detail were a function of the levels of enzyme activity. The colour of an apple fruit was determined by a number of factors. A major control point was one of the final steps in the flavonoid pathway (conversion of leucocyanidin to cyanidin) resulting in the synthesis, or lack of synthesis, of the anthocyanins. In all apple genotypes and cultivars examined the genes encoding for the enzymes responsible for catalysing this step must have been present, but the control was at the level of expression. Copigmentation is the bonding between anthocyanins and other phenolic molecules resulting in stabilization of the anthocyanin in its coloured form, a bathochromic shift and an increase in the absorbance of the visible band. In apples copigmentation probably had a role in stabilising anthocyanin colouration but did not influence colour variation because it was a constant factor. Self copigmentation may be occurring in some cultivars with high anthocyanin levels, resulting in blueing of the red colour. The intensity of the red colour was a function of the energy requirement for pigment synthesis, vacuolar size, pigment distribution and the influence of environmental factors. The major differences in hue were more likely to be due to the visual blending of chlorophyll, carotenoids and anthocyanins. Thus, the final appearance of the fruit was the result of the initial pigment concentrations plus the combined changes and hence the resultant final concentration of all three pigment groups (flavonoids, carotenoids and chlorophyll). The biochemical basis for fruit colour variation in apples has been determined but there are still some gaps in our knowledge particularly the control of flavonoid biosynthesis. The prospects for future genetic manipulation of apple fruit colour are discussed.