In obstructive sleep apnoea syndrome (OSAS), hypoxia secondary to repetitive apnoeic episodes leads to blood pressure variations and haemodynamic changes. There is also intermittent activation of the sympathetic system when the patient is aroused from sleep during apnoeic episodes. OSAS is known to be associated with many ophthalmological disorders such as floppy eyelid syndrome, glaucoma, non arteritic ischaemic optic neuropathy, central serous chorioretinopathy and papilloedema. However, little is known about the effects of OSAS on the choroid, one of the most vascularised tissues in the body. The aim of this study was to compare the choroidal thickness (CT) and retinal nerve fibre layer (RNFL) thickness in patients with OSAS to healthy controls. Ninety-two eyes of patients with OSAS and 32 eyes of age and body mass index (BMI) matched healthy controls were included in this study. OSAS patients were further divided into mild, moderate and severe groups according to their apnoea hypopnea index (AHI) values. All patients and controls were imaged with the RTVue SD-OCT system from 10am to 12am after pupil dilation. Measurements were taken for peripapillary RNFL thickness and macular CT and compared between groups. Results showed that the severe OSAS group had significantly thinner CT than the mild OSAS group at 3mm nasal to the fovea. The control group had significantly thicker CT 1.5mm and 3mm nasal to the fovea compared with the severe OSAS group. The severe and moderate OSAS groups had significantly thinner nasal RNFL measurements than controls. The severe OSAS group also had significantly thinner superior RNFL measurements than the controls. The authors conclude that patients with OSAS have choroidal structural alterations that may have significance on the pathophysiology of the ophthalmic disorders associated with OSAS.