Asphaltenes are naturally occurring components of crude oil and have been the subject of many studies that have involved a variety of methods to determine their complex structure, their association in crude oil with resins, and their agglomeration phenomena. Yet, the molecular structures of asphaltenes have not been fully elucidated. It is especially important to characterize the polar functionalities of these fractions, because they participate in the intermolecular aggregation by means of hydrogen bonds. The chemical derivatization of asphaltenes has been used, in combination with suitable analysis techniques, to study the influence of these heteroatom groups on molecular interactions within these fractions. Methylation and trimethyl silylation of five asphaltenes from different sources was performed in the laboratory as an effort to understand the molecular interactions within these fractions. Experimental data from isothermal titration calorimetry has been used in assessing the role of polar hydrogen bonding functionalities in self-association of these complex molecules. Stability characteristics of these altered asphaltenes have further been studied by onset flocculation titration and compared with data for starting (unaltered) asphaltenes. Changes at the molecular level were also investigated by infrared and fluorescence spectroscopy and size exclusion chromatography. It was observed that the asphaltenes that were most susceptible to these reaction chemistries were also the stable asphaltenes in crude oil. It has been inferred that the stability of these asphaltenes in crude oil definitely can be related to the extent of intrinsic polarity.