The choroidal vascularity index (CVI) is a new marker for the choroid. The decrease in CVI following latanoprost use can provide a better understanding of the pathogenesis of the posterior segment side effects of latanoprost such as cystoid macular edema and central serous choroidopathy.Purpose: The purpose of this paper is to evaluate the changes in the CVI, total choroidal area (TCA), stromal area (SA), luminal area (LA), and choroidal thickness (CT) following latanoprost therapy in patients with primary open angle glaucoma and ocular hypertension.Materials and Methods: Patients with newly diagnosed primary open angle glaucoma or ocular hypertension who had never received antiglaucoma therapy were included. Each patient received latanoprost 0.005% once daily. Enhanced depth imaging mode of spectral-domain optical coherence tomography scans was taken before the start of latanoprost therapy and in the first and third months. Subfoveal CT, CVI, TCA, LA, and SA for the submacular area, and 4 quadrants of the peripapillary area were calculated from the scans.Results: A total of 36 eyes of 18 patients were analyzed. Subfoveal CT increased significantly (P = 0.007). Mean TCA (P = 0.008) and SA (P < 0.001) in the first and third months were higher than baseline in the submacular regions. Mean CVI was lower in the first and third months (P < 0.001). There was an increase in the mean TCA and SA in the peripapillary temporal (P = 0.001 and 0.028) and inferior (P = 0.002 and <0.001) quadrants and a decrease in mean CVI in the temporal (P = 0.027) and inferior (P = 0.003) peripapillary quadrants. A negative correlation was found between the rate of decrease in intraocular pressure and the macular region CVI.Conclusions: Following latanoprost use for several months, the CVI was significantly decreased in newly treated patients with glaucoma or ocular hypertension, among other changes to the choroid. These findings may contribute to a better understanding of the effects of prostaglandins on the posterior segment of the eye.