The transport properties of 1,3-methylalkylimidazolium based ionic liquids are sensitive to their chemical structure. In this work, two key features of the chemical structure were investigated: the role of the anion and the length of the alkyl chain. Four different anions were examined for the 1,3-methylethylimidazolium salt (MeEtImX): bromide (Br'), iodide (I'), trifluoromethanesulfonate (Tf') and bis(trifluoromethanesulfonyl)amide (NTf2') anions. Increasing the size of the anion resulted in a decrease of the melting point and a slight increase in the cation diffusion coefficient. The differences in cation diffusion behaviour reflect the differences in viscosity, with much higher viscosities expected for the halide salts. In contrast to this diffusion behaviour, the melt conductivities are all very similar. The inconsistency between the calculated conductivity (based on diffusion measurements) and the conductivity measured, however, is attributed to correlated ion motions and/or the diffusion of neutral species that do not contribute to the conductivity. The effect of the length of the alkyl substituent was also studied for 1,3-methylalkylimidazolium iodide (MeRImI). Increasing the length of the alkyl chain, from methyl to a linear heptyl chain, suppresses the melting point and decreases both the conductivity and cation diffusion coefficients. In this case, the viscosity, as well as the size of the cation, influence ion transport in these materials.