The crystal and molecular structure and hydrogen bonding system in cellulose II have been revised using new neutron diffraction data extending to 1.2 Angstrom resolution collected from two highly crystalline fiber samples of mercerized flax, Mercerization was achieved in NaOH/H2O for one sample and in NaOD/D2O for the other, corresponding to the labile hydroxymethyl moieties being hydrogenated and deuterated, respectively. Fourier difference maps were calculated in which neutron difference amplitudes were combined with phases calculated from two revised X-ray models of cellulose II, A and B'. The revised phasing models were determined by refinement against the X-ray data set of Kolpak and Blackwell,(8) using the LALS methadology.(37) Both models A and B' have two antiparallel chains organized in a P2(1) space group and unit cell parameters: a = 8.01 Angstrom; b = 9.04 Angstrom, c = 10.36 Angstrom, and gamma = 117.1 degrees.(15) Model A has equivalent backbone conformations for both chains but different conformations for the hydroxymethyl moieties: gt for the origin chain and fg for the center chain. Model B', based on the recent crystal structures of cellotetraose,(21-23) has different conformations for the two chains but nearly equivalent conformations for the hydroxymethyl moieties. On the basis of the X-ray data alone, model A and model B' could not be differentiated. From the neutron Fourier difference maps, possible labile hydrogen atom positions were identified for each model and refined using LALS. We were able to eliminate model A in favor of model B'. The hydrogen-bonding scheme identified for model B' is significantly different from previous proposals based on the crystal structures of cellotetraose,(21-23) MD simulations of cellulose II,(25),and any potential hydrogen-bonding network in the structure of cellulose II determined in earlier X-ray fiber diffraction studies.(7,8) The exact localization of the labile hydrogen atoms involved in this bonding, together with their donor and acceptor characteristics, is presented and discussed. This study provides, for the first time, the coordinates of all of the atoms in cellulose II.