Purpose To determine microvascular changes in patients with genetically proven Marfan syndrome. Methods In a cross-sectional study, 32 eyes of 16 patients with genetically proven Marfan syndrome were evaluated using swept-source optical coherence tomography angiography (SS-OCTA). Patients were analyzed regarding lens status and systemic vascular disease. The foveal avascular zone (FAZ) and vessel density (VD) of the superficial and deep vascular plexus and central retinal thickness (CRT) were evaluated on SS-OCTA. Results 44/56% patients presented without/with subluxation of the lens. 69% of patients had presence of mitral valve insufficiency, aortic dilatation or aneurysm of the aortic root. In patients with Marfan syndrome the mean area of the FAZ was 0.2 ± 0.1 mm and the average VD of the superficial/deep vascular plexus was 36 ± 5%/22 ± 7%. In patients with subluxation of the lens FAZ area and perimeter were larger when compared to patients without subluxation of the lens (0.18 ± 0.08/0.28 ± 0.10 mm and 1.7 ± 0.4/2.3 ± 0.8; p = 0.02). VD of the superficial vascular plexus was reduced in patients with subluxation of the lens (on average 39 ± 3/33 ± 8; p = 0.01) together with an increased CRT in the inner segments of the ETDRS grid when compared to patients without subluxation of the lens. In patients with systemic vascular disease a larger FAZ area (0.19 ± 0.06/0.25 ± 0.1 mm; p = 0.04) and reduced VD of the superficial vascular plexus in the central ETDRS grid (28 ± 7/21 ± 6; p = 0.02) was observed in comparison to patients without systemic vascular changes. Conclusions In patients with Marfan syndrome SS-OCTA imaging revealed microvascular differences in patients with lens subluxation and/or systemic vascular disease.