The structural effects on DNA double helices of confinement in hydrophobic nanotubes (NT) with 30 and 40 angstrom diameters have been studied by classical molecular dynamics. For systems with the counter ions included inside the NT, there is little effect on the average DNA secondary structure relative to unconfined DNA. The DNA confined to the 40 angstrom NT shows little change in thermal fluctuations compared to unconfined DNA; however, a decrease is observed in the 30 angstrom NT. Finally, exclusion of ions from the NT leads to structures that deviate significantly from both canonical A- and B-DNA. Published by Elsevier B.V.