We have examined the aggregation behavior of a typical atmospheric residue feedstock by gel permeation chromatography (GPC). The size profiles for compounds containing sulfur, vanadium, and nickel were determined online from elemental detection by inductively coupled plasma (ICP) mass spectrometry. Four fractions that vary in aggregation state were analyzed by positive atmospheric pressure photoionization (APPI) 9.4 T Fourier transform ion cyclotron resonance mass spectrometry (APPI FT-ICR MS). Results showed an inverse relationship between fraction aggregate size and monomer ion yield and revealed that aggregation tendency did not correlate with higher polar or aromatic species abundance. Aggregation in the atmospheric residue more closely correlated with increased relative abundance of larger and more aliphatic compounds. The molecular composition of the GPC aggregate fractions suggests that nonpolar intermolecular forces between saturated, long-chain alkyl substituents contribute more to aggregation than pi-pi interactions.