The aim of the study was to assess longitudinal changes in the spatial relationship of the choroidal vasculature to retinal vasculature in myopic eyes. In the population-based longitudinal Beijing Eye Study in 2001/2011, we examined all highly myopic eyes with assessable fundus photographs and a randomized group of non-highly myopic. Using fundus photographs, we qualitatively assessed changes in the location of major choroidal vessels in relationship to retinal vessels. The study consisted of 85 highly myopic eyes (58 participants;age:64.8 +/- 9.4 years) and 85 randomly selected non-highly myopic eyes. A choroidal shift in relationship to the retinal vessels was detected more often in the highly myopic group than the non-highly myopic group (47/85 (55%) vs 6/85 (7%); P<0.001). In the highly myopic group, the choroidal vessel shift occurring on the disc-fovea line in 39 (44%) eyes, was similar to, or smaller than, the enlargement in gamma zone width in 26 (67%) eyes and in 11 (28%) eyes respectively. The choroidal vessel shift was larger (P=0.002) in eyes without choroidal vessels in gamma zone than in eyes with large choroidal vessels in gamma zone. In 14 (17%) eyes, a localized centrifugal choroidal shift was observed in association with an increase in the stage of myopic maculopathy. The results suggest that highly myopic eyes show a change in the position of large choroidal vessels in relationship to retinal vessels, in association with development or enlargement of gamma zone and an increase in the stage of myopic maculopathy.