The charge transport in a series of low band-gap copolymers based on the alternation of electron-rich units (thiophene, thienothiophene) and electron-deficient units (benzothiadiazole) and in their blends with a fullerene derivative (PCBM-C60) is investigated. The polymers are differentiated by the molecular structure of the conjugated backbone and by the nature, position and density of alkyl side chains. In pristine polymer films, the hole mobility has been investigated as a function of charge carrier density by analyzing the electrical response of field-effect transistors and single carrier spacecharge- limited current devices. By using the charge transport model developed by Vissenberg et al., we could quantify the structural disorder for the different polymers and correlate their degree of anisotropy with structural data obtained by Grazing Incidence Wide Angle X-ray diffraction. These polymers have been used in the active layer of organic solar cells. The ambipolar chargetransport was investigated in the corresponding polymer:fullerene blends. The results show that the side chains play a major role on the polymer: fullerene interactions and controls the optimal weight ratio. Also, we have shown that the nature of the side chains has a strong impact in the optimal electron conducting pathways.