Proanthocyanidins have a series of heteroflavan-3-ols, (+)-catechin/(-)-epicatechin units, which are linked through a single B-type linkage and a doubly linked A-type linkage. Recently, we have performed the structural characterization of seed shells of the Japanese horse chestnut and fruits of blueberry and cranberry. The molecular sizes of them were higher in the order of blueberry > cranberry > seed shells of the Japanese horse chestnut between the respective fractions. For the analysis of terminal and extension units in those proanthocyanidins, the isolated fractions were subjected to the thiolytic cleavage of the B-type linkages using 1-dodecanethiol, and the resulting degradation products were identified by ultraperformance liquid chromatography coupled with electrospray-ionization mass spectrometry. These analyses provided fast and good resolution of the degradation products and revealed higher proportions of A-type linkages compared with B-type linkages in both isolated fractions in the order of the seed shells > cranberry > blueberry. Moreover, the isolated fractions with higher molecular sizes and those more abundant in the proportions of A-type linkages were found to be more effective in the inhibition of pancreatic lipase activity. The results suggest that A-type highly polymeric proanthocyanidins are promising for the attenuation of lipid digestion as dietary supplements.