In nursery production of ornamental woody plants, rooting is routinely stimulated by application of auxin-containing rooting powders. This study compares various application methods of the indole-3-butyric acid (IBA) and their effects on rhizogenesis and investigates the mechanism of its action in stem cuttings of two cultivars of ninebark Physocarpus opulifolius Maxim. The cuttings were sprayed with water solution of IBA (50 mg l^-3), or their bases were treated with the commercial rooting powder Rhizopon AA (1% IBA), soaked 24 h in water solution after dissolving a Rhizopon AA tablet (50 mg l^-3) or immersed for 5 s in 150 mg l^-3 IBA (Rhizopon AA tablets – the „quick dip” method); untreated cuttings serving as controls were sprayed with water. Almost all treatments increased the rooting percentage in both cultivars tested. The effects of foliar IBA application and soaking the cuttings bases in the IBA solution (50 mg l^-3) were comparable to those of the commercial rooting powder. Auxin applications resulted in changes in the contents of several organic compounds in both tested cultivars: the levels of the chlorophyll content (a + b), total soluble sugars, free amino acids, and the indole-3-acetic acid were increased by some treatments while the levels of polyphenolic acids were reduced. The results of biochemical analyses indicate that the auxin preparations not only stimulate rhizogenesis but also affect the metabolism in cuttings, in a different way, depending on the application method and the cultivar.