In plants, ultraviolet (UV)-B acclimation is a complex, dynamic process that plays an essential role in preventing UV-B damage to targets such as DNA and the photosynthetic machinery. In this study we tested the hypothesis that the phytohormone auxin is a component of the regulatory system that controls both UV-mediated accumulation of flavonoids and UV-induced morphogenesis. We found that the leaf area of Arabidopsis thaliana Col-0 plants raised under a low dose of UV radiation (0.56 kJ m−2 daily dose) was, on average, decreased by 23% relative to plants raised in the absence of UV-B, and this was accompanied by a decrease (P = 0.063) in free auxin in young leaf tissues. Compared to Col-0, both the auxin influx mutant axr4-1 and the auxin biosynthesis mutant nit1-3 displayed significantly stronger morphogenic responses, i.e. relative decreases in leaf area were greater for these two mutants. UV exposure also induced accumulation of flavonoids. In Col-0, increases in the concentrations of specific kaempferol derivatives ranged from 2.1- to 19-fold. Thus, UV induces complex changes in flavonoid–glycosylation patterns. Compared to Col-0, three auxin mutants displayed significantly different flavonoid profiles. Thus, based on mutant analysis, it is concluded that the phytohormone auxin plays a role in UV acclimation by regulating flavonoid concentration, flavonoid–glycosylation pattern and by controlling UV-induced morphogenic responses.