An investigation of the refractive index and third-order nonlinear optical susceptibility chi(3) of two polypernigraniline derivatives, poly (4,4’-diphenylimine methine) (PDPIM) and poly(4,4’-diphenylimine p-heptyloxybenzylidene) (PDPIHB) reveals effects of molecular structure on the linear optical and nonlinear optical properties of conjugated polymers. The chi(3) (-3omega; omega, omega, omega) of PDPIM was found to decrease relative to polypemigraniline, reflecting the observed decrease of the oscillator strength of the 2.2 eV absorption band when a methine carbon replaces one of the nitrogen atoms of pernigraniline repeat unit. The alkoxyphenylene side group substitution at the methine carbon in PDPIHB, however, significantly enhances the nonlinear optical response of PDPIHB while reducing the refractive index compared to PDPIM and polypemigraniline. The present results suggest that structural changes in conjugated polymers can be made in such a way as to enhance the nonlinear optical properties while modulating the linear optical properties.