The authors describe a magneto-optic measurement system for the determination of Faraday rotation from ultrathin films relative to a substrate reference. The setup is intrinsically immune to reciprocal effects such as circular birefringence and thermal fluctuations. Faraday rotation measurements on thin films of 3-hexyl and 3-dodecyl derivatives of regioregular polythiophene are reported. The authors show that the Faraday rotation from these films is largely dependent on the supramolecular organization within the thin films of these polymers.