Carbon molecular sieve (CMS) membranes derived from polyimide (PI) and polyetherimide (PEI), which have similar functional groups were fabricated for gas separation. To evaluate the effect of the functional groups of PI and PEI on the properties of their CMS membranes, the composition of the casting solution and carbonization temperatures were investigated. Thermogravimetric analysis (TGA), fourier transform infrared spectroscopy (FTIR) and field emission scanning electron microscopy (FE-SEM) were employed to characterize thermal stability, functional groups and microstructural change in the derived CMS membrane. The gas permeation performance of the CMS membranes were estimated using four gases: hydrogen, carbon dioxide, nitrogen and methane. The results show that C=C stretching in imides exhibit an intense absorption peak at 1665 cm(-1) with PI dominating the insignificant degradation of the imide groups at the intermediate stage. For PEI, the absorption peaks of C=N stretching and C-C-C bending were intense at 1011 and 1068 cm(-1) respectively, dominating the ethers and cyclic ethers of asymmetric stretching. The microstructure and gas permeation properties of the obtained CMS membranes were significantly affected by the functional group of precursors and their concentrations in the casting solution. Optimized performance for hydrogen permeation (565 Barrer) [1 Barrer = 1 x 10(-10) cm(3) (STP) cm/(cm(2) s cmHg)] was obtained with PI-10-600 CMS membrane. The best selectivity for H-2/N-2 at 33.2 was obtained from PI-10-500 CMS membrane. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.