Background Since parapapillary atrophy and age-related macular degeneration (AMD) share features of their ophthalmoscopic and histological appearance, such as irregular pigmentation, proliferation and loss of the retinal pigment epithelium, it was the purpose of the study to assess whether parapapillary atrophy, particularly beta zone of parapapillary atrophy, is associated with AMD in a population-based investigation. Methods The Beijing Eye Study included 4439 subjects out of 5324 subjects invited to participate (response rate 83.4%) with an age of 40 + years. The present investigation consisted of 3874 (82.3%) subjects for whom readable fundus photographs of at least one eye were available with normal intraocular pressure, a refractive error of >- 8 diopters, and no signs of glaucomatous optic neuropathy. Results In a multivariate analysis, beta zone of parapapillary atrophy was significantly associated with age (P < 0.001), optic disc size (P < 0.001) and myopic refractive error (P < 0.001). It was not significantly associated with presence of retinal pigment depigmentation (P = 0.20) or hyperpigmentation (P = 0.99), drusen size (P = 0.27), and presence of early AMD (P = 0.72) or late AMD (P = 0.99). Conclusions Although beta zone of parapapillary atrophy and age-related macular degeneration have a similar histology with irregularities of the retinal pigment epithelium and eventual closure of the choriocapillaris and loss of retinal pigment epithelium cells, the entities are clinically not significantly associated with each other.