Skin autofluorescence (AF), a relatively simple and time saving procedure, measures the accumulation of advanced glycation end (AGE) products. The importance in autoimmune rheumatic diseases, particularly, systemic sclerosis (SSc), has not been evaluated yet. The aim of our study was to examine the skin AF in the context of SSc patients and to analyse the relations between skin AF and other surrogate measures of atherosclerosis. Forty-seven patients with SSc and 47 healthy volunteers were included in this study as controls. Patients and controls underwent common carotid artery wall assessment, arterial stiffness and wave reflection measurements, laser Doppler measurements of capillary flow, assessment of endothelial function by brachial ultrasound, peripheral arterial tonometry, and AGE measurement by skin AF. Wall properties of the common carotid arteries and wave reflection measurements were not affected in these study patients compared to controls while measures reflecting small capillary flow were altered. The accumulation of AGE products measured by skin AF was more prominent in SSc patients than in healthy controls. AGE products’ score was significantly associated with carotid radial pulse wave velocity, intima media/carotid artery diameter ratio, capillary flow percentage change during occlusion, and the disease itself in a multivariate linear analysis model.