Vertically-aligned carbon nanotube membranes have been fabricated and characterized and the corresponding gas permeability and hydrogen separation were measured. The carbon nanotube diameter and areal density were adjusted by varying the catalyst vapour concentration (Fe/C ratio) in the mixed precursor. The permeances are one to two magnitudes higher than the Knudsen prediction, while the gas selectivities are still in the Knudsen range. The diameter and areal density effects were studied and compared, the temperature dependence of permeation is also discussed. The results confirm the existence of non-Knudsen transport and that surface adsorption diffusion may affect the total permeance at relative low temperature. The permeance of aligned carbon nanotube membranes can be improved by increasing areal density and operating at an optimum temperature.