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In wheat, grain protein quantity is often inadequate for explaining flour quality, which is critical for determining sustainability of the milling and baking industry. Protein quality, referring to the concentrations and ratios of glutenin, gliadin and albumin protein fractions, is proving to be as important as protein quantity. South Africa has three production regions with specific cultivars developed for each region. Size exclusion high performance liquid chromatography was used to separate protein fractions in commercial wheat cultivars for each of the three regions. Two locations and two seasons for each region were analysed. The highest concentration of glutenin was seen in wheat from the rainfed winter rainfall region, a/ß, ? gliadin in wheat from the rainfed summer rainfall region and albumin/globulin in irrigated wheat. No consistent trends for concentrations and ratios of protein fractions could be established, nor consistent correlations with major baking quality parameters in the three production regions. Large insoluble glutenins of irrigated and rainfed summer rainfall wheat cultivars only correlated highly positively with flour protein, whereas in rainfed wheat of the winter rainfall region large insoluble glutenin correlated highly positively with flour protein, grain protein and loaf volume. Insoluble small glutenin proteins of irrigated wheat correlated highly positively with low loaf volume, whereas in the rainfed summer rainfall cultivars small soluble and insoluble glutenin correlated negatively with low loaf volume. In rainfed wheat from the winter rainfall region, small insoluble glutenin in total protein correlated negatively with grain protein, but positively with loaf volume. Protein fractions were therefore not consistent predictors of good baking quality, as both environment and genotype largely influenced this relationship.