This paper presents results from the first analyses of the mesostructure of natural rubber (NR) by asymmetrical flow field flow fractionation (AF4). The results are compared with those obtained by size exclusion chromatography (SEC) in terms of average molar masses, radius of gyration and insoluble part (or gel quantity). Comparable results were obtained for the sample not containing gel. Conversely, for samples with gel, significant differences were found due to the presence of microaggregates. Contrary to SEC, AF4 fractionation enables partial fractionation of polyisoprene chains and microaggregates in a single run without preliminary treatment. The results presented here also highlight the special structure (very compact spheres) of microaggregates in NR compared to chemical crosslinked microaggregates in synthetic polyisoprene. The advantages and drawbacks of both techniques for analysing NR samples are also discussed.