To investigate the retinal vascular findings and associated cystoid edema in the central macula of eyes with retinal vein occlusion using volume-rendered angiographic and structural optical coherence tomography. Observational case series. In this retrospective study 12 eyes of 12 consecutive patients, 3 with branch and 9 with central retinal vein occlusion, were imaged in 27 sessions with optical coherence tomography (OCT) using split-spectrum amplitude decorrelation. The structural OCT data were segmented for cystoid spaces and integrated into the angiographic data for subsequent volume rendering. The inner and deep vascular plexus were analyzed in relation to cystoid macular edema with retention of depth information. Retinal vascular flow abnormalities were demonstrated by flow voids with abnormal vascular morphology in the inner vascular layer and varying flow loss in the deep vascular plexus. Areas of cystoid edema were associated with topographically co-localizing flow voids in the deep vascular layer. Treatment with intravitreous anti-vascular endothelial growth factor injections resulted in resolution of edema but no change in flow patterns in either the inner or deep plexus. Recurrence of edema happened in the same areas of altered inner and absent deep vascular plexus flow signal. Cystoid macular edema in retinal vein occlusion occurred in relation to altered inner plexus and absent deep vascular plexus flow. This pattern of cystoid fluid accumulation is similar to that seen in diabetic retinopathy and may represent an important underlying pathophysiologic foundation for cystoid macular edema in retinal vascular diseases.