Mass spectrometry using selected ion monitoring, high-performance liquid chromatography and an Amaranthus betacyanin bioassay enabled six endogenous cytokinins to be identified from potato (Solanum tuberosum L. cv. Danshaku) tubers, and their levels to be determined. The six cytokinin species were cis- and trans-ribofuranosyl zeatin (RZ), cis- and trans-zeatin (Z), 9-β-D-ribofuranosyl 6-(3-methyl-2-butenylamino)purine (i6Ado), and a new glucopyranosyl derivative of i6Ade, 9-β-D-glucopyranosyl 6-(3-methyl-2-butenylamino)purine (i6AG). Using deuterium-labeled standards, their levels were determined: cis-RZ (55.34%) was the most abundant, followed by i6AG (11.57%), i6Ado, trans-RZ (3.72%), trans-Z (1.24%), and cis-Z (0.41%). It is presumed that cis-RZ is a "functional" cytokinin species playing a causative role in potato tuberization, whereas trans-RZ plays a positive role in sweet potato tuberization, which may be explained by potato tubers deriving from stems and sweet potato tubers from roots.