In this work, the amphiphilic isoindigo (am-iInd) based conjugated polymers namely poly(am-iInd-DT) and poly(am-iInd-TT) and their regular counterpart poly(reg-iInd-DT) and poly(reg-iInd-TT) were synthesized to compare their opto-electronic and charge transport properties. They were used to fabricate organic field effect transistors. Charge transport properties in conjugated polymers depend upon intermolecular interaction which is strongly affected by the nature of side chains. The amphiphilic nature of the conjugated polymers has little impact on the charge transport properties. The charge carrier mobility of amphiphilic conjugated polymers was comparable with the regular polymers except poly(reg-iInd-DT) which can be correlated by X-ray diffraction and thin film morphology. (c) 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 45461.