This work summarizes some results obtained through equilibrium molecular dynamic simulations regarding the structure and transport properties of several ionic liquids (ILs). The Green–Kubo relationships were employed to evaluate the cation/anion diffusion coefficients, electrical conductivity and shear viscosity at 400 K. The ILs investigated were 1-ethyl-3-methylimidazolium salts of Cl−, NO3 − and PF6 − using two different force fields for the cation: a rigid ion model of 1-ethyl-3-methylimidazolium, studied in a previous work [C. Rey-Castro, L.F. Vega, J. Phys. Chem. B 110 (2006) 14426–14435] and the flexible model of Urahata and Ribeiro [S.M. Urahata, M.C.C. Ribeiro, J. Chem. Phys. 120 (2004) 1855–1863]. Regarding the anions, the most evident difference between the local structures in the three ILs is the position of the first peak of the radial distribution function, reflecting the differences in anion sizes and shapes. The velocity autocorrelation functions are particularly sensitive to the relative weights of anion and cation, although the integrated self-diffusion coefficients do not show significant differences between the Cl−, NO3 − and PF6 − salts. The electric conductivity predicted by the rigid ion model of [emim]Cl is lower than the experimental value, whereas the model overestimates the viscosities. In contrast, the flexible model leads to diffusion rates and conductivities that are one order of magnitude higher at the same temperature. The shear viscosities obtained from simulations of the flexible model are in very good agreement with experimental data. The calculated conductivities are compared with values obtained from the diffusion coefficients through the Nernst–Einstein relation in order to determine the importance of cross-correlation among ions. The stress tensor and the distinct van Hove correlation functions indicate that the dynamics of the local structure of the fluid relaxes faster in the flexible model.