The oxidation stability of biodiesel composed of fatty acid esters derived from vegetable oils, is one of the major issues affecting its wide-spread incorporation as an alternative fuel. The poor oxidative stability of biodiesel compared to petrodiesel, originates specifically from its high content of unsaturated fatty acid methyl esters. Moreover, the relationship between new oxidative molecular structures and resulting solution morphologies is a complex subject that affects physico-chemical properties of the fuel. The goal of this work was to understand how the oxidized unsaturated fatty acid methyl esters and the non-oxidized components of the biodiesel interact and affect the final properties of multicomponent biodiesel mixtures. Towards this objective standard pure fatty acid methyl esters and biodiesel mixtures were heated for different time periods with constant stirring to induce autoxidation, and then analyzed by 1H low field nuclear magnetic resonance (LF-NMR) relaxometry. To further define the molecular consequence of autoxidation and appearance of autoxidation products, a combination of supporting methods, including, gas chromatography, mass spectrometry, Fourier transform infrared, 1H high field NMR, and thermogravimetric analysis were applied. 1H LF-NMR relaxometry was proven to be an advantageous tool to probe autoxidation of biodiesel. For example we describe in this paper the interactive effect of new oxidative products and stable non-oxidized components upon each other`s molecular movement and morphology during the process of oxidation. One major result was to show that the oxidized products of fatty acid methyl esters have different secondary interactions between themselves and the biodiesel components which were not oxidized but are mutually affected by each other. Characterizing these changes in molecular interactions and how they affect biodiesel properties is one of the major contributions of 1H LF-NMR relaxometry.