Mechanical or thermal mastication experiments were performed on three commercial natural rubber (NR) samples of TSR10 grade made from latex of three different clones (GT1, PB235, and RRIM600). The mesostructure (different gel or aggregate fractions, structure of random coils of cis-1,4-polyisoprene) of all the NR samples was fully characterized by size exclusion chromatography coupled with multiangle light scattering (SEC-MALS), using pretreated SEC columns. This method was used to quantify and investigate the structure of the little-studied smaller microaggregates, constituting the microgel fraction smaller than 1 µm (Microgel<1µ) of NR. The three unmasticated NR samples showed no difference in terms of microaggregate structure. Conversely, microaggregates appeared denser after mastication. This phenomenon was found to depend on the mastication conditions, as mechanically masticated NR samples had smaller (lower radius of gyration) and more compact microaggregates than thermally masticated samples. Macrogel also behaved differently depending on the mastication conditions. Mechanical mastication conditions allowed a higher degradation of the macrogel compared with thermal mastication conditions.