The influence of process-induced pectin changes on the kinematic viscosity of the serum phases of carrot and tomato purées was investigated in this study. Variations in the amount of pectin present in the serum phase and pectin’s fine structure were induced by subjecting carrot and tomato to different thermal treatments, i.e. a mild and a strong heat treatment, followed by blending and high-pressure homogenisation at different pressure levels (0, 20 and 100 MPa). Changes in pectin structure were monitored by determination of the degree of methoxylation, analysing the molar mass distribution and immuno-dot blotting using anti-pectin antibodies. Characterisation of serum pectins revealed that a strong thermal treatment caused pectin thermosolubilisation and depolymerisation, especially in carrot sera, and high-pressure homogenisation provoked predominantly mechanical pectin solubilisation in carrot sera and pectin depolymerisation in tomato sera. It was observed that the kinematic viscosity of carrot sera was mainly affected by the amount of solubilised pectin, whereas in tomato sera, the kinematic viscosity could mainly be explained in terms of polysaccharide chain length. The degree of methoxylation of pectin, which has a broader distribution in tomato sera than in carrot sera, seemed to have a less pronounced role in determining the kinematic viscosity. In general, it could be concluded that serum viscosity is mainly determined by the amount and size of the solubilised pectin. The influence of serum viscosity on the rheology of the studied purées was limited as the rheology of this type of system is largely determined by the particle properties of the dispersed phase.