Purpose: To assess the choroidal thickness in differently pigmented areas of the fundus in a 46-year-old female with Waardenburg syndrome. Methods: Retrospective, case review. Choroidal thickness was measured using swept-source optical coherence tomography (SS-OCT, Topcon DRI OCT-1 Atlantis) and compared between the pigmented and hypopigmented areas within the same eye and between the two eyes. Results: Best corrected visual acuity (BCVA) was 20/20 in both eyes. The right fundus had a variegated appearance without choroidal hypopigmentation. The left fundus had choroidal hypopigmentation beyond the superotemporal arcade up to the periphery. Subfoveal choroidal thickness was 455 µ in the right eye and 569 µ in the left eye. In the left eye, the comparison of two equidistant points from the foveola along a radial scan passing through the superotemporal hypopigmented area revealed a thinner choroidal thickness (457 µ) compared to the corresponding point in the pigmented inferonasal quadrant (591 µ). Conclusion: Choroidal thickness is decreased in the hypopigmented area of the fundus compared to the pigmented area in subjects with Waardenburg syndrome. The overall thickness of the choroid in such eyes could still be more than the mean value in the normal population.