During fruit and vegetable processing, procyanidins interact with cell walls and form complexes, which further impact their potential health effects. Among cell wall polysaccharides, pectins have the highest affinity for procyanidins. Binding of two procyanidin fractions with twelve pectins of different linearity and size was investigated by ITC, UV–Visible spectrophotometry and HPSEC-MALLS. Pectins interacted preferentially with highly polymerized procyanidins except beet pectins probably because of steric hindrance due to abundant feruloylated arabinans. Linear pectins had higher affinity for procyanidins: this was verified both for comparison between botanical origins (kiwifruit > apple > beet pectins) and between extraction conditions. Debranched pectins, extracted at pH 2.0, had higher affinity and aggregation capacities with procyanidins than those extracted at other pHs. However, the factors affecting pectins of different origins seemed to be different. High molar mass, intrinsic viscosity and hydrodynamic radius contributed more to increased adsorption of procyanidins by apple and beet pectins. Highly linear kiwifruit pectins, with high homogalacturonan content and lowerbranching ratio bound preferentially to procyanidins. The enthalpy/entropy proportion of the interaction between kiwifruit pectins and procyanidins was higher than that of apple and beet pectins, which suggested more hydrogen bonding. Predominance of homogalacturonan regions and high degree of methylation thus appeared key structural features of pectins for high affinity for procyanidins, while high degree of branching was detrimental. These findings provide the structural foundation for selectivity of interactions in molecular-level.