A series of semifluorinated 3-alkylthiophenes ((3-thienyl-(CH2)(m)-CF2)(n)F, Th-m,n) were prepared by addition of perfluoroalkyl iodides to 3-(omega-alken-1-yl)thiophenes followed by treatment with NaBH4. Chemical and electrochemical oxidation gave the corresponding substituted polythiophenes. The fluorinated side chains have dramatic effects on the conjugation of the polythiophene backbone and thermal phase behavior. Since the perfluoroalkyl parts of the side chains are approximately the same size as alkyl parts, and the electron-withdrawing effect of the fluorine atoms is insulated from the thiophene ring by a hydrocarbon spacer, these effects are ascribed to interactions between side chains. Microsegregation arising from the immiscibility of fluorocarbon and hydrocarbon segments of semifluorinated alkyl-substituted polymers provides for control of supermolecular architecture. The new 3-(semifluorinated alkyl)thiophenes will serve as comonomers in the design of self-organizing conjugated polymers.