Here we report the quantum yield of four aggregated perylene diimide (PDI) species that vary by the length of the branched side chains attached at the N,N' imide positions. The PDI molecules were dissolved in binary water:methanol solvents as a means to vary the solvent polarity and control the degree of aggregation in solution. By performing spectroscopy, kinetics, and light scattering experiments, the nature of the molecular interactions in the solutions was determined. The maximum quantum yield of the aggregated molecules increased from 0.04 for the shortest chain molecule (B2) to 0.20 for the largest chain molecule (B13). The higher quantum yield of B13 compared with B2 correlates well with an increase in the fluorescence lifetime. The monomer emission lifetime was 4.8 ns whereas a lifetime as high as 21.2 ns was measured for the B13 aggregate fluorescence. A shorter sub-nanosecond lifetime was also measured for suspended colloids in B5, B9, and B13. The enhanced quantum yield is attributed to an increase of disorder in the B13 aggregates. As the polarity of the solution increases, the hydrophobic effect further enhances the disorder, and, therefore, the quantum yields in these particles.