We present a new method to automatically segment the thickness of the choroid in the human eye by polarization sensitive optical coherence tomography (PS-OCT). A swept source PS-OCT instrument operating at a center wavelength of 1040 nm is used. The segmentation method is based entirely on intrinsic, tissue specific polarization contrast mechanisms. In a first step, the anterior boundary of the choroid, the retinal pigment epithelium, is segmented based on depolarization. In a second step, the choroid-sclera interface is found by using the birefringence of the sclera. The method is demonstrated in five healthy eyes. The mean repeatability (standard deviation) of thickness measurement was found to be 18.3 µm.