The invention generally relates to a polarization sensitive optical coherence tomography (OCT) system that includes both polarization maintaining and single mode optical fiber and methods of use thereof. Generally, OCT systems of the invention have a light source and a differential path interferometer that includes a sample arm and a reference arm. A splitter is used to split light from the light source to the sample arm and the reference arm. Reflected light from the sample arm and the reference arm is recombined at a detector. The polarization maintaining fiber is used in the reference arm to ensure that optical field intensity is equalized between two orthogonal detection channels of the OCT system.