Functionalized carbon nanotubes (f-CNTs) are explored as novel nanomaterials for biomedical applications. UV-vis luminescence of aqueous dispersions of CNT-NH3+ and CNT-NH-Ac (NH-Ac: acetamido) is observed using standard laboratory spectrophotometric instrumentation, and the measured fluorescence intensity is correlated with the aggregation state of the f-CNTs: a high intensity indicates improved f-CNT individualization and dispersion, while a decrease in fluorescence intensity indicates a higher degree of nanotube aggregation and bundling as a result of varying the sodium dodecyl sulfate (SDS) concentrations and pH in the aqueous phase. Moreover, utilization of this relationship between fluorescence intensity and the state of f-CNT aggregation is carried out to elucidate the interactions between f-CNTs and gene-encoding plasmid DNA (pDNA). pDNA is shown to interact with CNT-NH 3+ primarily through electrostatic interactions that lead concomitantly to a higher degree of f-CNT bundling. The CNT-NH3 +/pDNA interactions are successfully competed by SDS/f-CNT surface interactions, resulting in the displacement of pDNA. These studies provide exemplification of the use of fluorescence spectrophotometry to accurately describe the aggregation state of water-soluble f-CNTs. Characterization of the complexes between pDNA and f-CNTs elucidates the opportunities and limitations of such supramolecular systems as potential vectors for gene transfer. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.