Two families of naphthalene diimide (NDI) derivatives were compared and contrasted for the effect of self-assembly on charge carrier transport. One series of NDI derivatives had a terminal phenyl ring attached to a hexyl spacer substituted naphthalene core either through an ester or an amide linkage (NDI-E and NDI-A, respectively), while the other series had a 3,4,5-tridodecyloxy phenyl unit (NDI-E3, NDI-A3) instead of the terminal phenyl unit. Solution processed thin films of these molecules exhibited n-type charge transport characteristics in a bottom gate top contact organic field effect transistor (OFET) geometry. The amide derivatives showed evidence of self-organization with observation of red shifted aggregate emission in solution as well as solid state. Variable temperature FTIR studies in the solid state confirmed the existence of strong hydrogen bonding which could be broken only at very high temperature. However, contrary to expectations, the NDI ester derivatives showed better device efficiency with electron mobilities in the range 8.5 x 10(-3) to 2 x 10(-2) cm(2) V-1 s(-1) and on/off ratio similar to 10(4). The thin film crystallinity and morphology of NDI-E and NDI-A were examined through X-ray diffraction and atomic force microscopy (AFM). The correlation of crystallinity, hydrogen bonding and charge carrier mobility was studied using energy minimized structures from density functional theory (DFT). The higher electron mobility of ester linked NDI derivatives over the amide linked ones was attributed to the freedom in charge transport pathways offered by a three dimensional crystalline organization in the ester compared to the restricted directional hydrogen bonding interaction in the amide derivatives.