Semivolatile and nonpolar organic compounds, such as persistent organic pollutants, have a tendency to accumulate in organic matter phases from air and water. Once they enter living systems, they partition into lipids/waxes and can exert adverse toxicological effects. The current paradigm assumes that such chemicals are uniformly distributed in organic phases such as soil organic matter, plant waxes, and animal lipids and that partitioning and adsorption processes occur independently of intermolecular contaminant interactions. With use of a recently developed technique, two-photon excitation microscopy coupled with autofluorescence allowed us to directly visualize novel organic chemical behavior in living vegetation and other matrixes. Here, we show for the first time that polycyclic aromatic hydrocarbons, which were uniformly distributed in pure oils and waxes at the beginning of a study, form clusters over time. The number and diameter (typically 0.2−5 μm) of these clusters are dependent on the physical-chemical properties of the compound-media systems and time. This behavior is not accounted for in current models of phase partitioning of chemicals and may have important implications for understanding their environmental fate and their potential toxicological effects.