Differential guest-binding behavior was observed between two pyrene-edged Fe4L6 cages, prepared from isomeric bis(4-aminophenyl)pyrene derivatives, 2-formylpyridine and iron(II). The cage based on a 1,6-pyrene scaffold possesses an enclosed cavity suitable for the encapsulation of large hydrophobic guests including fullerenes, polycyclic aromatic hydrocarbons, and large, structurally complex natural products such as steroids. Addition of the fullerenes C60 and C70 to the cage brought about a re-equilibration among the different cage diastereomers in order to maximize the binding affinity of the system. Density functional theory was employed to rationalize the experimentally observed energy differences for C60 binding within the cage diastereomers. In contrast, the cage isomer based on a 2,7-pyrene scaffold has a more porous cavity and did not show affinity for neutral hydrophobic guests.