With the goal of identifying an improved delivery scheme for intracellular tracking and anticancer therapy, we explored a novel double functionalization of a carbon nanotube delivery system containing antisense oligodeoxynucleotides (ASODNs) as a therapeutic gene and CdTe quantum dots as fluorescent labeling probes via electrostatically layer-by-layer assembling. This is the first time that we used mercaptoacetic acid-capped CdTe quantum dots as fluorescent labeling probes for clearly tracking the intracellular transport and evaluating delivery efficiency of ASODNs by functionalized multiwalled carbon nanotubes (MWNTs).