The auxin and phenolic contents, as well as phenylalanine ammonia-lyase (PAL) activity, were determined in in vitro cultured shoots of the recalcitrant-to-root rac mutant of tobacco, and compared with wild-type shoots. The mutant and wild-type shoots showed similar auxin changes during the culture cycle, but with higher contents for the mutant. A transient peak of auxin (corresponding to the achievement of the rooting inductive phase) occurred at day 14 in both types of shoots, but earlier in the basal parts of the wild-type stems. The rac shoots contained more phenolics, corresponding with an increased PAL activity. The most abundant phenolic compound found in the two types of tobacco was chlorogenic acid, which was more abundant in the rac shoots. Rutin was also detected at a higher concentration in the mutant shoots. Basal parts of wild-type shoots treated with 10–3 M chlorogenic acid reacted by accumulating auxins and, unlike untreated controls, did not form adventitious roots. The relationships between these biochemical analyses in relation to the growth limitation of the rac mutant, and the inhibition of its root development, are discussed.