Gel-permeation chromatography (GPC) has been used to analyze transition-metal-based squares, triangles, and related supramolecular complexes. Using rhenium-containing molecular squares of different sizes, a linear calibration curve has been established, which was used for confirming the relative sizes of other assemblies. GPC can also discriminate cyclic trimers and tetramers of a dirhodium building block. Preparative GPC has been used to resolve macroscopic samples of a rhenium-based supramolecular mixture into pure syn and anti isomers. A mixture of "triangle" and "square" has also been successfully separated.