CdSe/CdS dot/rods nanocrystals show interesting physical properties related to the band-alignment at the hetero-interface, which controls the band-edge electron delocalization over the rods. Here the differential transmission spectra of CdSe/CdS nanorod samples with different core sizes have been measured using excitation resonant to the core transition. The photo bleaching ratio between dot and rod transitions increases with the dot size, indicating a trend towards electron localization. This trend has been further quantified by performing effective mass calculations in which the conduction band misalignment was varied in order to reproduce the observed bleaching feature ratio. The best agreement was found for negligible conduction band misalignment for small dots of around 2.3 nm in diameter, and about -0.1 eV misalignment was estimated for the larger dots, above 3.5 nm in diameter. This shows that the band misalignment might be dependent on the geometry of the system, and we argue that this might be related to different strain developed at the hetero-interface.