We investigate the effect of the choice of the basis set on the results of ab initio (density functional theory/non-equilibrium Green’s function) calculations of the bandgap of semiconducting carbon nanotubes, and near-zero-bias conductance of metallic carbon nanotubes. Both ideal and deformed carbon nanotubes are studied, as well as nanotubes with an adsorbed biomolecule. The results show that the near-zero-bias conductance of armchair nanotubes can be calculated accurately with a minimal basis set, with the exception of the (2,2) tube, where a polarized basis set is necessary to accurately predict the metallic behaviour of this tube. For zigzag tubes, a double-zeta polarized basis set is in general required for accuracy in bandgap and near-zero-bias conductance calculations.