The sidewalls of vertically aligned, multiwalled carbon nanotubes were functionalized using azide photochemistry, and DNA oligonucleotides were synthesized in situ from the reactive group on each photoadduct to produce water-soluble DNA-coated nanotubes. The functional DNA sites on the nanotubes were visualized from gold nanoparticles modified with complementary DNA and using TEM. The sidewall functionalization enabled further DNA-directed modification of the nanotubes' surfaces with nanoparticles. The DNA-coated vertically aligned nanotubes offer the architecture for a highly loaded three-dimensional DNA chip.