Nuclease effects on the cell internalization of single-walled carbon nanotubes (SWNTs) functionalized with fluorescent-labeled DNA in serum containing cell growth media were examined. When Cy3-labeled DNA-functionalized SWNT conjugates (Cy3DNA-SWNTs) were incubated with HeLa cells in a fatal bovine serum (FBS) medium, a high fluorescence intensity was obtained from the cells, indicative for the high level inclusion of Cy3DNA-SWNTs. However, the fluorescence intensity was remarkably reduced if Cy3DNA-SWNTs were incubated with cells in the FBS-free medium. Further systematic control experiments revealed that Cy3 dye molecules were released from Cy3DNA-SWNT conjugates by nuclease, and the free Cy3 dyes penetrate into HeLa cell with high efficiency. Although the actual amounts of SWNTs internalized in the cells were almost identical for both cells incubated in the FBS-present and FBS-absent media according to the Raman measurements, one should be cautious to determine the degree of SWNT internalization based on the fluorescence intensities especially when the coloring dye molecules were linked to oligonucleotides in nuclease containing media.