The excited state properties of cyanine dyes and the orientations of their aggregates were studied using density functional theory (DFT). The effects of exchange-correlation functional and solvent model on the absorption spectrum of Cy5 was investigated. Using the 6-31+G(d,p) basis set and B3LYP exchange-correlation functional with IEF-PCM (water) solvent, the predicted spectrum achieved a maximum absorbance within 0.007 eV of experiment. An in-house program based on the theoretical model of Kühn, Renger, and May (KRM), which predicts the orientation of dyes within an aggregate from its absorbance and circular dichroism (CD) spectra or vice versa, was used to investigate the orientation of an experimentally observed dimer. The absorbance spectrum predicted using the KRM model of the dimer structure optimized with the 6-31+G(d,p) basis set, ωB97XD exchange-correlation functional, and IEF-PCM solvent agrees with experimental data.